Genetic Variant ENSG00000287092:n.225-4418A>G (chr6-156299172-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 ENST00000663591.1(ENSG00000287092):n.225-4418A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.448 in 151,940 control chromosomes in the GnomAD database, including 15,800 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 0.45 ( 15800 hom., cov: 32)

Consequence

ENSG00000287092
ENST00000663591.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.71

Publications

3 publications found

Variant links:

Genes affected

ENSG00000287092 (HGNC:):

ENSG00000287092 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=-1.05).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.534 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000287092	ENST00000663591.1 link	n.225-4418A>G	intron_variant	Intron 1 of 3
ENSG00000287092	ENST00000789128.1 link	n.309-4418A>G	intron_variant	Intron 2 of 3
ENSG00000287092	ENST00000789132.1 link	n.325-4418A>G	intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes

AF:

0.448

AC:

68069

AN:

151822

Hom.:

15780

Cov.:

show subpopulations

Gnomad AFR

AF:

0.540

Gnomad AMI

AF:

0.193

Gnomad AMR

AF:

0.328

Gnomad ASJ

AF:

0.294

Gnomad EAS

AF:

0.496

Gnomad SAS

AF:

0.497

Gnomad FIN

AF:

0.516

Gnomad MID

AF:

0.358

Gnomad NFE

AF:

0.415

Gnomad OTH

AF:

0.419

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

GnomAD4 genome

AF:

0.448

AC:

68140

AN:

151940

Hom.:

15800

Cov.:

AF XY:

0.452

AC XY:

33565

AN XY:

74256

show subpopulations

African (AFR)

AF:

0.540

AC:

22378

AN:

41452

American (AMR)

AF:

0.328

AC:

5006

AN:

15280

Ashkenazi Jewish (ASJ)

AF:

0.294

AC:

1020

AN:

3470

East Asian (EAS)

AF:

0.496

AC:

2565

AN:

5168

South Asian (SAS)

AF:

0.496

AC:

2387

AN:

4816

European-Finnish (FIN)

AF:

0.516

AC:

5442

AN:

10554

Middle Eastern (MID)

AF:

0.367

AC:

108

AN:

294

European-Non Finnish (NFE)

AF:

0.415

AC:

28167

AN:

67890

Other (OTH)

AF:

0.423

AC:

891

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1915

3829

5744

7658

9573

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

632

1264

1896

2528

3160

<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:

0.443

Hom.:

3584

Bravo

AF:

0.434

Asia WGS

AF:

0.531

AC:

1842

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.1

CADD

Benign

0.54

(source)

DANN

Benign

0.58

PhyloP100

-2.7

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