dbSNP rs2596517: ENSG00000297040:n.120+2877G>A (chr6-31392318-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 ENST00000744920.1(ENSG00000297040):n.120+2877G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.848 in 151,740 control chromosomes in the GnomAD database, including 54,869 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 0.85 ( 54869 hom., cov: 32)

Consequence

ENSG00000297040
ENST00000744920.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.25

Publications

8 publications found

Variant links:

Genes affected

ENSG00000297040 (HGNC:):

ENSG00000297040 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=-1.02).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.929 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000297040	ENST00000744920.1 link	n.120+2877G>A	intron_variant	Intron 1 of 2
ENSG00000297040	ENST00000744921.1 link	n.92-67G>A	intron_variant	Intron 1 of 1
MICA-AS1	ENST00000745027.1 link	n.567+7736C>T	intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.848

AC:

128638

AN:

151624

Hom.:

54817

Cov.:

show subpopulations

Gnomad AFR

AF:

0.830

Gnomad AMI

AF:

0.922

Gnomad AMR

AF:

0.898

Gnomad ASJ

AF:

0.930

Gnomad EAS

AF:

0.951

Gnomad SAS

AF:

0.940

Gnomad FIN

AF:

0.840

Gnomad MID

AF:

0.927

Gnomad NFE

AF:

0.829

Gnomad OTH

AF:

0.880

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

GnomAD4 genome

AF:

0.848

AC:

128745

AN:

151740

Hom.:

54869

Cov.:

AF XY:

0.852

AC XY:

63197

AN XY:

74146

show subpopulations

African (AFR)

AF:

0.830

AC:

34228

AN:

41214

American (AMR)

AF:

0.899

AC:

13653

AN:

15194

Ashkenazi Jewish (ASJ)

AF:

0.930

AC:

3218

AN:

3460

East Asian (EAS)

AF:

0.951

AC:

4915

AN:

5166

South Asian (SAS)

AF:

0.940

AC:

4523

AN:

4812

European-Finnish (FIN)

AF:

0.840

AC:

8884

AN:

10582

Middle Eastern (MID)

AF:

0.925

AC:

272

AN:

294

European-Non Finnish (NFE)

AF:

0.829

AC:

56351

AN:

67998

Other (OTH)

AF:

0.882

AC:

1860

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1005

2010

3015

4020

5025

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

892

1784

2676

3568

4460

<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:

0.833

Hom.:

7442

Bravo

AF:

0.850

Asia WGS

AF:

0.936

AC:

3252

AN:

3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

5.4

(source)

DANN

Benign

0.48

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