Genetic Variant ENSG00000288782:n.113-6860C>T (chr8-2176139-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 ENST00000685917.3(ENSG00000288782):n.113-6860C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.136 in 152,128 control chromosomes in the GnomAD database, including 1,854 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 0.14 ( 1854 hom., cov: 33)

Consequence

ENSG00000288782
ENST00000685917.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.544

Publications

0 publications found

Variant links:

Genes affected

ENSG00000288782 (HGNC:):

ENSG00000288782 links:

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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=-0.89).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.297 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105377781	XR_941356.3 link	n.108-16796C>T		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000288782	ENST00000685917.3 link	n.113-6860C>T	intron_variant	Intron 1 of 1
ENSG00000288782	ENST00000776942.1 link	n.130-16796C>T	intron_variant	Intron 1 of 3
ENSG00000288782	ENST00000776943.1 link	n.128-8812C>T	intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes

AF:

0.136

AC:

20695

AN:

152010

Hom.:

1851

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0312

Gnomad AMI

AF:

0.110

Gnomad AMR

AF:

0.120

Gnomad ASJ

AF:

0.183

Gnomad EAS

AF:

0.242

Gnomad SAS

AF:

0.310

Gnomad FIN

AF:

0.235

Gnomad MID

AF:

0.114

Gnomad NFE

AF:

0.166

Gnomad OTH

AF:

0.127

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

GnomAD4 genome

AF:

0.136

AC:

20707

AN:

152128

Hom.:

1854

Cov.:

AF XY:

0.143

AC XY:

10601

AN XY:

74378

show subpopulations

African (AFR)

AF:

0.0311

AC:

1294

AN:

41548

American (AMR)

AF:

0.120

AC:

1828

AN:

15288

Ashkenazi Jewish (ASJ)

AF:

0.183

AC:

635

AN:

3468

East Asian (EAS)

AF:

0.242

AC:

1249

AN:

5166

South Asian (SAS)

AF:

0.310

AC:

1496

AN:

4822

European-Finnish (FIN)

AF:

0.235

AC:

2477

AN:

10552

Middle Eastern (MID)

AF:

0.112

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.166

AC:

11316

AN:

67966

Other (OTH)

AF:

0.132

AC:

279

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

900

1800

2701

3601

4501

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

254

508

762

1016

1270

<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:

0.0801

Hom.:

307

Bravo

AF:

0.119

Asia WGS

AF:

0.214

AC:

744

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

1.8

(source)

DANN

Benign

0.82

PhyloP100

0.54

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