dbSNP rs112018640: ATR:p.Tyr1956Tyr (chr3-142496391-G-A) – ACMG Classification: Benign (-19 pts)

Variant summary

Our verdict is Benign. The variant received -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BS1BS2

The NM_001184.4(ATR):c.5868C>T(p.Tyr1956Tyr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00964 in 1,549,054 control chromosomes in the GnomAD database, including 289 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.011 ( 21 hom., cov: 28)

Exomes 𝑓: 0.0096 ( 268 hom. )

Consequence

ATR
NM_001184.4 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:11

Conservation

PhyloP100: 0.817

Publications

10 publications found

Variant links:

Genes affected

ATR (HGNC:882): (ATR serine/threonine kinase) The protein encoded by this gene is a serine/threonine kinase and DNA damage sensor, activating cell cycle checkpoint signaling upon DNA stress. The encoded protein can phosphorylate and activate several proteins involved in the inhibition of DNA replication and mitosis, and can promote DNA repair, recombination, and apoptosis. This protein is also important for fragile site stability and centrosome duplication. Defects in this gene are a cause of Seckel syndrome 1. [provided by RefSeq, Aug 2017]

ATR Gene-Disease associations (from GenCC):

Seckel syndrome 1
Inheritance: AR Classification: DEFINITIVE, STRONG Submitted by: G2P, Ambry Genetics, Illumina
familial cutaneous telangiectasia and oropharyngeal predisposition cancer syndrome
Inheritance: AD, Unknown Classification: MODERATE, SUPPORTIVE, LIMITED Submitted by: Genomics England PanelApp, Labcorp Genetics (formerly Invitae), Orphanet
sarcoma
Inheritance: AD Classification: MODERATE Submitted by: Genomics England PanelApp
Seckel syndrome
Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
familial prostate carcinoma
Inheritance: AD Classification: LIMITED Submitted by: Ambry Genetics

ATR links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -19 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.44).

BP6

Variant 3-142496391-G-A is Benign according to our data. Variant chr3-142496391-G-A is described in ClinVar as Benign. ClinVar VariationId is 157996.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=0.817 with no splicing effect.

BS1

Variant frequency is greater than expected in population sas. GnomAd4 allele frequency = 0.0105 (1433/136252) while in subpopulation SAS AF = 0.0246 (102/4140). AF 95% confidence interval is 0.0208. There are 21 homozygotes in GnomAd4. There are 665 alleles in the male GnomAd4 subpopulation. Median coverage is 28. This position passed quality control check.

BS2

High Homozygotes in GnomAd4 at 21 AD,Unknown,AR gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001184.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ATR	NM_001184.4	MANE Select	c.5868C>T	p.Tyr1956Tyr	synonymous	Exon 34 of 47	NP_001175.2	Q13535-1
	ATR	NM_001354579.2		c.5676C>T	p.Tyr1892Tyr	synonymous	Exon 33 of 46	NP_001341508.1	Q13535-2

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
ATR	ENST00000350721.9	TSL:1 MANE Select	c.5868C>T	p.Tyr1956Tyr	synonymous	Exon 34 of 47	ENSP00000343741.4	Q13535-1
ATR	ENST00000513291.2	TSL:1	n.1052C>T		non_coding_transcript_exon	Exon 4 of 16
ATR	ENST00000936442.1		c.5715C>T	p.Tyr1905Tyr	synonymous	Exon 33 of 46	ENSP00000606501.1

Frequencies

GnomAD3 genomes

AF:

0.0105

AC:

1433

AN:

136164

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0115

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00708

Gnomad ASJ

AF:

0.0201

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.0251

Gnomad FIN

AF:

0.000770

Gnomad MID

AF:

0.00769

Gnomad NFE

AF:

0.0113

Gnomad OTH

AF:

0.00980

GnomAD2 exomes

AF:

0.00920

AC:

2268

AN:

246470

AF XY:

0.0102

show subpopulations

Gnomad AFR exome

AF:

0.00719

Gnomad AMR exome

AF:

0.00576

Gnomad ASJ exome

AF:

0.0126

Gnomad EAS exome

AF:

0.000109

Gnomad FIN exome

AF:

0.00199

Gnomad NFE exome

AF:

0.00927

Gnomad OTH exome

AF:

0.00933

GnomAD4 exome

AF:

0.00956

AC:

13505

AN:

1412802

Hom.:

268

Cov.:

AF XY:

0.0101

AC XY:

7105

AN XY:

702812

show subpopulations

African (AFR)

AF:

0.00784

AC:

253

AN:

32276

American (AMR)

AF:

0.00575

AC:

250

AN:

43516

Ashkenazi Jewish (ASJ)

AF:

0.0137

AC:

337

AN:

24612

East Asian (EAS)

AF:

0.0000525

AC:

AN:

38126

South Asian (SAS)

AF:

0.0243

AC:

2018

AN:

83088

European-Finnish (FIN)

AF:

0.00193

AC:

AN:

51240

Middle Eastern (MID)

AF:

0.0192

AC:

104

AN:

5410

European-Non Finnish (NFE)

AF:

0.00914

AC:

9848

AN:

1076890

Other (OTH)

AF:

0.0103

AC:

594

AN:

57644

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.437

Heterozygous variant carriers

565

1130

1695

2260

2825

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

400

800

1200

1600

2000

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.0105

AC:

1433

AN:

136252

Hom.:

Cov.:

AF XY:

0.0102

AC XY:

665

AN XY:

65312

show subpopulations

African (AFR)

AF:

0.0115

AC:

423

AN:

36682

American (AMR)

AF:

0.00707

AC:

AN:

12580

Ashkenazi Jewish (ASJ)

AF:

0.0201

AC:

AN:

3284

East Asian (EAS)

AF:

0.00

AC:

AN:

4492

South Asian (SAS)

AF:

0.0246

AC:

102

AN:

4140

European-Finnish (FIN)

AF:

0.000770

AC:

AN:

7790

Middle Eastern (MID)

AF:

0.00847

AC:

AN:

236

European-Non Finnish (NFE)

AF:

0.0113

AC:

727

AN:

64328

Other (OTH)

AF:

0.00971

AC:

AN:

1854

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.449

Heterozygous variant carriers

134

178

223

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

100

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0160

Hom.:

ClinVar

ClinVar submissions

Significance:Benign

Revision:criteria provided, multiple submitters, no conflicts

View on ClinVar

Pathogenic

VUS

Benign

Condition

not provided (5)

Familial cutaneous telangiectasia and oropharyngeal predisposition cancer syndrome (2)

not specified (2)

Seckel syndrome 1 (2)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.44

CADD

Benign

(source)

DANN

Benign

0.39

PhyloP100

0.82

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over