dbSNP rs17840762: HSPA5-DT:n.46G>A (chr9-125241708-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000468244.3(HSPA5-DT):n.46G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.108 in 158,532 control chromosomes in the GnomAD database, including 1,138 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.11 ( 1106 hom., cov: 32)

Exomes 𝑓: 0.087 ( 32 hom. )

Consequence

HSPA5-DT
ENST00000468244.3 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.04

Publications

5 publications found

Variant links:

Genes affected

HSPA5-DT (HGNC:55645): (HSPA5 divergent transcript)

HSPA5-DT links:

Genome browser will be placed here

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=-0.73).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.184 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000468244.3. 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
	HSPA5-DT	NR_186826.1		n.53G>A		non_coding_transcript_exon	Exon 1 of 3

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank
HSPA5-DT	ENST00000468244.3	TSL:4	n.46G>A	non_coding_transcript_exon	Exon 1 of 4
HSPA5-DT	ENST00000761981.1		n.72G>A	non_coding_transcript_exon	Exon 1 of 3
HSPA5-DT	ENST00000761982.1		n.40G>A	non_coding_transcript_exon	Exon 1 of 4

Frequencies

GnomAD3 genomes

AF:

0.109

AC:

16542

AN:

152036

Hom.:

1106

Cov.:

show subpopulations

Gnomad AFR

AF:

0.187

Gnomad AMI

AF:

0.0725

Gnomad AMR

AF:

0.0605

Gnomad ASJ

AF:

0.104

Gnomad EAS

AF:

0.154

Gnomad SAS

AF:

0.118

Gnomad FIN

AF:

0.0973

Gnomad MID

AF:

0.114

Gnomad NFE

AF:

0.0707

Gnomad OTH

AF:

0.0961

GnomAD4 exome

AF:

0.0872

AC:

557

AN:

6384

Hom.:

Cov.:

AF XY:

0.0871

AC XY:

297

AN XY:

3410

show subpopulations

African (AFR)

AF:

0.235

AC:

AN:

170

American (AMR)

AF:

0.0313

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.121

AC:

AN:

240

East Asian (EAS)

AF:

0.148

AC:

AN:

528

South Asian (SAS)

AF:

0.0899

AC:

AN:

434

European-Finnish (FIN)

AF:

0.103

AC:

AN:

620

Middle Eastern (MID)

AF:

0.105

AC:

AN:

European-Non Finnish (NFE)

AF:

0.0706

AC:

277

AN:

3926

Other (OTH)

AF:

0.0693

AC:

AN:

332

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.510

Heterozygous variant carriers

105

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<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:

0.109

AC:

16569

AN:

152148

Hom.:

1106

Cov.:

AF XY:

0.111

AC XY:

8226

AN XY:

74374

show subpopulations

African (AFR)

AF:

0.188

AC:

7777

AN:

41460

American (AMR)

AF:

0.0603

AC:

922

AN:

15294

Ashkenazi Jewish (ASJ)

AF:

0.104

AC:

362

AN:

3470

East Asian (EAS)

AF:

0.154

AC:

794

AN:

5166

South Asian (SAS)

AF:

0.119

AC:

575

AN:

4828

European-Finnish (FIN)

AF:

0.0973

AC:

1031

AN:

10594

Middle Eastern (MID)

AF:

0.116

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0707

AC:

4809

AN:

68018

Other (OTH)

AF:

0.0941

AC:

199

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.498

Heterozygous variant carriers

739

1478

2217

2956

3695

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

178

356

534

712

890

<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:

0.128

Hom.:

330

Bravo

AF:

0.110

Asia WGS

AF:

0.133

AC:

461

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.73

CADD

Benign

0.23

(source)

DANN

Benign

0.92

PhyloP100

-1.0

PromoterAI

0.019

Neutral

(source)

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.0

Mutation Taster

=99/1

polymorphism

(source)

Splicing

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