dbSNP rs10492756: ENSG00000301273:n.402+52211G>A (chr16-7753015-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000777597.1(ENSG00000301273):n.402+52211G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.119 in 114,878 control chromosomes in the GnomAD database, including 635 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 0.12 ( 635 hom., cov: 30)

Consequence

ENSG00000301273
ENST00000777597.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.26

Publications

4 publications found

Variant links:

Genes affected

ENSG00000301273 (HGNC:):

ENSG00000301273 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=-0.95).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.141 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000301273	ENST00000777597.1 link	n.402+52211G>A		intron_variant	Intron 3 of 3
ENSG00000301273	ENST00000777598.1 link	n.310+52211G>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes

AF:

0.119

AC:

13677

AN:

114786

Hom.:

634

Cov.:

show subpopulations

Gnomad AFR

AF:

0.145

Gnomad AMI

AF:

0.0583

Gnomad AMR

AF:

0.0813

Gnomad ASJ

AF:

0.146

Gnomad EAS

AF:

0.00873

Gnomad SAS

AF:

0.0872

Gnomad FIN

AF:

0.179

Gnomad MID

AF:

0.110

Gnomad NFE

AF:

0.116

Gnomad OTH

AF:

0.102

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.119

AC:

13704

AN:

114878

Hom.:

635

Cov.:

AF XY:

0.119

AC XY:

6652

AN XY:

55666

show subpopulations

African (AFR)

AF:

0.146

AC:

3332

AN:

22894

American (AMR)

AF:

0.0812

AC:

962

AN:

11844

Ashkenazi Jewish (ASJ)

AF:

0.146

AC:

466

AN:

3194

East Asian (EAS)

AF:

0.00875

AC:

AN:

2630

South Asian (SAS)

AF:

0.0869

AC:

322

AN:

3706

European-Finnish (FIN)

AF:

0.179

AC:

1413

AN:

7880

Middle Eastern (MID)

AF:

0.123

AC:

AN:

268

European-Non Finnish (NFE)

AF:

0.116

AC:

6930

AN:

59876

Other (OTH)

AF:

0.101

AC:

171

AN:

1694

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

649

1298

1948

2597

3246

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

160

320

480

640

800

<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:

0.101

Hom.:

698

Bravo

AF:

0.0838

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.95

CADD

Benign

0.74

(source)

DANN

Benign

0.21

PhyloP100

-1.3

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over