dbSNP rs6500291: ENSG00000260381:n.125+917A>G (chr16-50120902-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000566770.1(ENSG00000260381):n.125+917A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.362 in 152,082 control chromosomes in the GnomAD database, including 12,476 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 0.36 ( 12476 hom., cov: 32)

Consequence

ENSG00000260381
ENST00000566770.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.463

Publications

6 publications found

Variant links:

Genes affected

ENSG00000260381 (HGNC:):

ENSG00000260381 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=-0.53).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.645 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
ENSG00000260381	ENST00000566770.1 link	n.125+917A>G	intron_variant	Intron 1 of 2	3
ENSG00000287444	ENST00000657788.1 link	n.92+747T>C	intron_variant	Intron 1 of 1
ENSG00000260381	ENST00000832508.1 link	n.263-14250A>G	intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes

AF:

0.361

AC:

54913

AN:

151964

Hom.:

12441

Cov.:

show subpopulations

Gnomad AFR

AF:

0.652

Gnomad AMI

AF:

0.233

Gnomad AMR

AF:

0.288

Gnomad ASJ

AF:

0.344

Gnomad EAS

AF:

0.307

Gnomad SAS

AF:

0.261

Gnomad FIN

AF:

0.143

Gnomad MID

AF:

0.263

Gnomad NFE

AF:

0.250

Gnomad OTH

AF:

0.338

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

GnomAD4 genome

AF:

0.362

AC:

54993

AN:

152082

Hom.:

12476

Cov.:

AF XY:

0.353

AC XY:

26250

AN XY:

74360

show subpopulations

African (AFR)

AF:

0.652

AC:

27036

AN:

41470

American (AMR)

AF:

0.288

AC:

4390

AN:

15262

Ashkenazi Jewish (ASJ)

AF:

0.344

AC:

1195

AN:

3472

East Asian (EAS)

AF:

0.307

AC:

1588

AN:

5172

South Asian (SAS)

AF:

0.259

AC:

1248

AN:

4822

European-Finnish (FIN)

AF:

0.143

AC:

1514

AN:

10606

Middle Eastern (MID)

AF:

0.265

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.250

AC:

17020

AN:

67962

Other (OTH)

AF:

0.337

AC:

712

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1546

3092

4639

6185

7731

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

498

996

1494

1992

2490

<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:

0.268

Hom.:

6059

Bravo

AF:

0.391

Asia WGS

AF:

0.295

AC:

1028

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.53

CADD

Benign

(source)

DANN

Benign

0.93

PhyloP100

0.46

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