dbSNP rs11987758: ENSG00000288782:n.113-2416G>A (chr8-2180583-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 ENST00000685917.3(ENSG00000288782):n.113-2416G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.12 in 152,192 control chromosomes in the GnomAD database, including 1,109 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 ( 1109 hom., cov: 32)

Consequence

ENSG00000288782
ENST00000685917.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.355

Publications

3 publications found

Variant links:

Genes affected

ENSG00000288782 (HGNC:):

ENSG00000288782 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 = 0.144 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105377781	XR_941356.3 link	n.108-12352G>A		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000288782	ENST00000685917.3 link	n.113-2416G>A	intron_variant	Intron 1 of 1
ENSG00000288782	ENST00000776942.1 link	n.130-12352G>A	intron_variant	Intron 1 of 3
ENSG00000288782	ENST00000776943.1 link	n.128-4368G>A	intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes

AF:

0.121

AC:

18331

AN:

152072

Hom.:

1110

Cov.:

show subpopulations

Gnomad AFR

AF:

0.147

Gnomad AMI

AF:

0.0747

Gnomad AMR

AF:

0.104

Gnomad ASJ

AF:

0.0801

Gnomad EAS

AF:

0.131

Gnomad SAS

AF:

0.0943

Gnomad FIN

AF:

0.117

Gnomad MID

AF:

0.123

Gnomad NFE

AF:

0.112

Gnomad OTH

AF:

0.134

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

GnomAD4 genome

AF:

0.120

AC:

18322

AN:

152192

Hom.:

1109

Cov.:

AF XY:

0.119

AC XY:

8852

AN XY:

74408

show subpopulations

African (AFR)

AF:

0.147

AC:

6086

AN:

41518

American (AMR)

AF:

0.104

AC:

1586

AN:

15296

Ashkenazi Jewish (ASJ)

AF:

0.0801

AC:

278

AN:

3470

East Asian (EAS)

AF:

0.131

AC:

674

AN:

5160

South Asian (SAS)

AF:

0.0939

AC:

453

AN:

4822

European-Finnish (FIN)

AF:

0.117

AC:

1236

AN:

10604

Middle Eastern (MID)

AF:

0.126

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.112

AC:

7625

AN:

68006

Other (OTH)

AF:

0.132

AC:

279

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

824

1647

2471

3294

4118

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

202

404

606

808

1010

<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:

0.119

Hom.:

2367

Bravo

AF:

0.120

Asia WGS

AF:

0.123

AC:

427

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.95

CADD

Benign

3.4

(source)

DANN

Benign

0.25

PhyloP100

0.35

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