Variant 20-3667815-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The variant allele was found at a frequency of 0.868 in 152,194 control chromosomes in the GnomAD database, including 57,506 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 0.87 ( 57461 hom., cov: 32)

Exomes 𝑓: 0.83 ( 45 hom. )

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0420

Variant links:

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ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.82).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.905 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes

AF:

0.868

AC:

131967

AN:

151950

Hom.:

57431

Cov.:

show subpopulations

Gnomad AFR

AF:

0.852

Gnomad AMI

AF:

0.861

Gnomad AMR

AF:

0.917

Gnomad ASJ

AF:

0.874

Gnomad EAS

AF:

0.733

Gnomad SAS

AF:

0.906

Gnomad FIN

AF:

0.807

Gnomad MID

AF:

0.870

Gnomad NFE

AF:

0.884

Gnomad OTH

AF:

0.882

GnomAD4 exome

AF:

0.833

AC:

105

AN:

126

Hom.:

AF XY:

0.824

AC XY:

AN XY:

102

show subpopulations

Gnomad4 AFR exome

AF:

1.00

Gnomad4 AMR exome

AF:

0.500

Gnomad4 ASJ exome

AF:

1.00

Gnomad4 SAS exome

AF:

0.950

Gnomad4 FIN exome

AF:

0.889

Gnomad4 NFE exome

AF:

0.792

Gnomad4 OTH exome

AF:

0.833

GnomAD4 genome

AF:

0.868

AC:

132051

AN:

152068

Hom.:

57461

Cov.:

AF XY:

0.866

AC XY:

64344

AN XY:

74326

show subpopulations

Gnomad4 AFR

AF:

0.852

Gnomad4 AMR

AF:

0.917

Gnomad4 ASJ

AF:

0.874

Gnomad4 EAS

AF:

0.733

Gnomad4 SAS

AF:

0.905

Gnomad4 FIN

AF:

0.807

Gnomad4 NFE

AF:

0.884

Gnomad4 OTH

AF:

0.880

Alfa

AF:

0.880

Hom.:

11741

Bravo

AF:

0.875

Asia WGS

AF:

0.842

AC:

2927

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

4.3

DANN

Benign

0.75

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over