Genetic Variant ENSG00000288587:n.62+19427G>C (chr6-31420190-G-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000673857.1(ENSG00000288587):n.62+19427G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.107 in 151,408 control chromosomes in the GnomAD database, including 1,327 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 0.11 ( 1327 hom., cov: 31)

Consequence

ENSG00000288587
ENST00000673857.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.212

Publications

20 publications found

Variant links:

Genes affected

ENSG00000288587 (HGNC:):

ENSG00000288587 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=-0.78).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.332 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000288587	ENST00000673857.1 link	n.62+19427G>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.107

AC:

16235

AN:

151292

Hom.:

1321

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0285

Gnomad AMI

AF:

0.0374

Gnomad AMR

AF:

0.171

Gnomad ASJ

AF:

0.145

Gnomad EAS

AF:

0.345

Gnomad SAS

AF:

0.215

Gnomad FIN

AF:

0.151

Gnomad MID

AF:

0.127

Gnomad NFE

AF:

0.107

Gnomad OTH

AF:

0.112

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

GnomAD4 genome

AF:

0.107

AC:

16243

AN:

151408

Hom.:

1327

Cov.:

AF XY:

0.114

AC XY:

8470

AN XY:

74020

show subpopulations

African (AFR)

AF:

0.0285

AC:

1170

AN:

41098

American (AMR)

AF:

0.171

AC:

2588

AN:

15100

Ashkenazi Jewish (ASJ)

AF:

0.145

AC:

503

AN:

3466

East Asian (EAS)

AF:

0.345

AC:

1765

AN:

5116

South Asian (SAS)

AF:

0.214

AC:

1025

AN:

4800

European-Finnish (FIN)

AF:

0.151

AC:

1595

AN:

10562

Middle Eastern (MID)

AF:

0.126

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.107

AC:

7283

AN:

67952

Other (OTH)

AF:

0.115

AC:

243

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

686

1372

2057

2743

3429

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

180

360

540

720

900

<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:

0.0449

Hom.:

Bravo

AF:

0.106

Asia WGS

AF:

0.269

AC:

936

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.78

CADD

Benign

9.7

(source)

DANN

Benign

0.88

PhyloP100

0.21

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