dbSNP rs2970077: ATMIN:c.-293A>G (chr16-81041195-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000566488.1(ATMIN):c.-293A>G variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.881 in 706,352 control chromosomes in the GnomAD database, including 278,827 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as (no stars).

Frequency

Genomes: 𝑓 0.80 ( 51036 hom., cov: 32)

Exomes 𝑓: 0.90 ( 227791 hom. )

Consequence

ATMIN
ENST00000566488.1 5_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.381

Publications

13 publications found

Variant links:

Genes affected

ATMIN (HGNC:29034): (ATM interactor) Enables dynein complex binding activity. Involved in positive regulation of transcription, DNA-templated. Located in nuclear body. [provided by Alliance of Genome Resources, Apr 2022]

ATMIN links:

ENSG00000284512 (HGNC:):

ENSG00000284512 links:

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new If you want to explore the variant's impact on the transcript ENST00000566488.1, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.89).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.942 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000566488.1. 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
	ATMIN	NM_015251.3	MANE Select	c.337-161A>G		intron	N/A	NP_056066.2
	ATMIN	NM_001300728.2		c.-132-161A>G		intron	N/A	NP_001287657.1	O43313-2

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
ATMIN	ENST00000566488.1	TSL:1	c.-293A>G	5_prime_UTR	Exon 1 of 3	ENSP00000455497.1	O43313-2
ATMIN	ENST00000299575.5	TSL:1 MANE Select	c.337-161A>G	intron	N/A	ENSP00000299575.3	O43313-1
ATMIN	ENST00000564241.5	TSL:1	c.-132-161A>G	intron	N/A	ENSP00000463478.1	O43313-2

Frequencies

GnomAD3 genomes

AF:

0.799

AC:

121487

AN:

152068

Hom.:

51030

Cov.:

show subpopulations

Gnomad AFR

AF:

0.502

Gnomad AMI

AF:

0.973

Gnomad AMR

AF:

0.903

Gnomad ASJ

AF:

0.918

Gnomad EAS

AF:

0.930

Gnomad SAS

AF:

0.964

Gnomad FIN

AF:

0.845

Gnomad MID

AF:

0.896

Gnomad NFE

AF:

0.917

Gnomad OTH

AF:

0.856

GnomAD4 exome

AF:

0.904

AC:

500829

AN:

554166

Hom.:

227791

Cov.:

AF XY:

0.908

AC XY:

261417

AN XY:

287816

show subpopulations

African (AFR)

AF:

0.497

AC:

6851

AN:

13774

American (AMR)

AF:

0.931

AC:

15164

AN:

16290

Ashkenazi Jewish (ASJ)

AF:

0.919

AC:

12456

AN:

13554

East Asian (EAS)

AF:

0.926

AC:

27333

AN:

29530

South Asian (SAS)

AF:

0.966

AC:

43543

AN:

45074

European-Finnish (FIN)

AF:

0.859

AC:

34989

AN:

40754

Middle Eastern (MID)

AF:

0.925

AC:

1945

AN:

2102

European-Non Finnish (NFE)

AF:

0.914

AC:

333388

AN:

364858

Other (OTH)

AF:

0.891

AC:

25160

AN:

28230

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

2139

4278

6416

8555

10694

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

3646

7292

10938

14584

18230

<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:

0.798

AC:

121518

AN:

152186

Hom.:

51036

Cov.:

AF XY:

0.801

AC XY:

59598

AN XY:

74394

show subpopulations

African (AFR)

AF:

0.501

AC:

20772

AN:

41460

American (AMR)

AF:

0.903

AC:

13805

AN:

15294

Ashkenazi Jewish (ASJ)

AF:

0.918

AC:

3186

AN:

3472

East Asian (EAS)

AF:

0.930

AC:

4823

AN:

5186

South Asian (SAS)

AF:

0.965

AC:

4656

AN:

4826

European-Finnish (FIN)

AF:

0.845

AC:

8957

AN:

10602

Middle Eastern (MID)

AF:

0.891

AC:

262

AN:

294

European-Non Finnish (NFE)

AF:

0.917

AC:

62363

AN:

68028

Other (OTH)

AF:

0.856

AC:

1807

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

986

1971

2957

3942

4928

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

856

1712

2568

3424

4280

<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:

0.883

Hom.:

77871

Bravo

AF:

0.788

Asia WGS

AF:

0.923

AC:

3208

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

4.4

(source)

DANN

Benign

0.68

PhyloP100

-0.38

Mutation Taster

=300/0

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

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