Genetic Variant ENSG00000295781:n.199-4902G>C (chr3-193757480-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 ENST00000732702.1(ENSG00000295781):n.199-4902G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.432 in 152,012 control chromosomes in the GnomAD database, including 16,552 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 0.43 ( 16552 hom., cov: 32)

Consequence

ENSG00000295781
ENST00000732702.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.123

Publications

2 publications found

Variant links:

Genes affected

ENSG00000295781 (HGNC:):

ENSG00000295781 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=-0.95).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.698 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
ENSG00000295781	ENST00000732702.1 link	n.199-4902G>C		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes

AF:

0.431

AC:

65519

AN:

151894

Hom.:

16516

Cov.:

show subpopulations

Gnomad AFR

AF:

0.704

Gnomad AMI

AF:

0.283

Gnomad AMR

AF:

0.369

Gnomad ASJ

AF:

0.308

Gnomad EAS

AF:

0.479

Gnomad SAS

AF:

0.453

Gnomad FIN

AF:

0.274

Gnomad MID

AF:

0.446

Gnomad NFE

AF:

0.308

Gnomad OTH

AF:

0.413

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

GnomAD4 genome

AF:

0.432

AC:

65618

AN:

152012

Hom.:

16552

Cov.:

AF XY:

0.428

AC XY:

31779

AN XY:

74292

show subpopulations

African (AFR)

AF:

0.705

AC:

29201

AN:

41448

American (AMR)

AF:

0.369

AC:

5629

AN:

15272

Ashkenazi Jewish (ASJ)

AF:

0.308

AC:

1070

AN:

3470

East Asian (EAS)

AF:

0.480

AC:

2480

AN:

5170

South Asian (SAS)

AF:

0.452

AC:

2174

AN:

4808

European-Finnish (FIN)

AF:

0.274

AC:

2890

AN:

10562

Middle Eastern (MID)

AF:

0.452

AC:

132

AN:

292

European-Non Finnish (NFE)

AF:

0.308

AC:

20906

AN:

67964

Other (OTH)

AF:

0.415

AC:

878

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1684

3367

5051

6734

8418

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

590

1180

1770

2360

2950

<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:

0.214

Hom.:

454

Bravo

AF:

0.450

Asia WGS

AF:

0.496

AC:

1723

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

4.0

(source)

DANN

Benign

0.67

PhyloP100

0.12

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