dbSNP rs2467350: ENSG00000296959:n.377-9606A>C (chr15-36480608-A-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000743889.1(ENSG00000296959):n.377-9606A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.35 in 152,110 control chromosomes in the GnomAD database, including 9,484 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 0.35 ( 9484 hom., cov: 32)

Consequence

ENSG00000296959
ENST00000743889.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.274

Publications

2 publications found

Variant links:

Genes affected

ENSG00000296959 (HGNC:):

ENSG00000296959 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=-1.01).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.461 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105370768	XR_932110.1 link	n.249-4310A>C		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000296959	ENST00000743889.1 link	n.377-9606A>C	intron_variant	Intron 2 of 3
ENSG00000296959	ENST00000743890.1 link	n.239-9606A>C	intron_variant	Intron 2 of 3
ENSG00000296959	ENST00000743891.1 link	n.253-9606A>C	intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.350

AC:

53238

AN:

151990

Hom.:

9471

Cov.:

show subpopulations

Gnomad AFR

AF:

0.327

Gnomad AMI

AF:

0.329

Gnomad AMR

AF:

0.470

Gnomad ASJ

AF:

0.378

Gnomad EAS

AF:

0.321

Gnomad SAS

AF:

0.251

Gnomad FIN

AF:

0.379

Gnomad MID

AF:

0.324

Gnomad NFE

AF:

0.341

Gnomad OTH

AF:

0.379

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

GnomAD4 genome

AF:

0.350

AC:

53283

AN:

152110

Hom.:

9484

Cov.:

AF XY:

0.352

AC XY:

26150

AN XY:

74344

show subpopulations

African (AFR)

AF:

0.326

AC:

13538

AN:

41496

American (AMR)

AF:

0.471

AC:

7197

AN:

15294

Ashkenazi Jewish (ASJ)

AF:

0.378

AC:

1311

AN:

3470

East Asian (EAS)

AF:

0.321

AC:

1658

AN:

5172

South Asian (SAS)

AF:

0.252

AC:

1215

AN:

4828

European-Finnish (FIN)

AF:

0.379

AC:

4003

AN:

10552

Middle Eastern (MID)

AF:

0.321

AC:

AN:

290

European-Non Finnish (NFE)

AF:

0.341

AC:

23165

AN:

67986

Other (OTH)

AF:

0.380

AC:

804

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1782

3564

5345

7127

8909

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

526

1052

1578

2104

2630

<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:

0.342

Hom.:

38346

Bravo

AF:

0.359

Asia WGS

AF:

0.347

AC:

1206

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

6.9

(source)

DANN

Benign

0.70

PhyloP100

0.27

Splicing

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

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

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