Genetic Variant ENSG00000301139:n.238+2923G>A (chr17-34248950-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 ENST00000776537.1(ENSG00000301139):n.238+2923G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.156 in 152,068 control chromosomes in the GnomAD database, including 2,253 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 0.16 ( 2253 hom., cov: 32)

Consequence

ENSG00000301139
ENST00000776537.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.775

Publications

12 publications found

Variant links:

Genes affected

ENSG00000301139 (HGNC:):

ENSG00000301139 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 (NFE) allele frequency at 95% confidence interval = 0.218 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000301139	ENST00000776537.1 link	n.238+2923G>A	intron_variant	Intron 2 of 2
ENSG00000301139	ENST00000776538.1 link	n.238+2923G>A	intron_variant	Intron 2 of 2
ENSG00000301139	ENST00000776539.1 link	n.236+2923G>A	intron_variant	Intron 2 of 2
ENSG00000301139	ENST00000776540.1 link	n.158+2923G>A	intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes

AF:

0.156

AC:

23699

AN:

151950

Hom.:

2252

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0634

Gnomad AMI

AF:

0.118

Gnomad AMR

AF:

0.113

Gnomad ASJ

AF:

0.212

Gnomad EAS

AF:

0.0853

Gnomad SAS

AF:

0.0934

Gnomad FIN

AF:

0.214

Gnomad MID

AF:

0.0981

Gnomad NFE

AF:

0.221

Gnomad OTH

AF:

0.138

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

GnomAD4 genome

AF:

0.156

AC:

23699

AN:

152068

Hom.:

2253

Cov.:

AF XY:

0.153

AC XY:

11357

AN XY:

74328

show subpopulations

African (AFR)

AF:

0.0633

AC:

2625

AN:

41484

American (AMR)

AF:

0.113

AC:

1720

AN:

15280

Ashkenazi Jewish (ASJ)

AF:

0.212

AC:

737

AN:

3470

East Asian (EAS)

AF:

0.0851

AC:

440

AN:

5170

South Asian (SAS)

AF:

0.0937

AC:

451

AN:

4814

European-Finnish (FIN)

AF:

0.214

AC:

2259

AN:

10556

Middle Eastern (MID)

AF:

0.105

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.221

AC:

15042

AN:

67980

Other (OTH)

AF:

0.136

AC:

287

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1009

2017

3026

4034

5043

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

264

528

792

1056

1320

<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:

0.190

Hom.:

512

Bravo

AF:

0.144

Asia WGS

AF:

0.0810

AC:

285

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.78

CADD

Benign

(source)

DANN

Benign

0.79

PhyloP100

0.78

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