20-3775950-T-C

Variant names:

• chr20-3775950-T-C
• rs13043330

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.61 in 152,074 control chromosomes in the GnomAD database, including 28,355 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 0.61 (28355 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.422
• Publications: 19 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.612 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.610 AC: 92649 AN: 151956 Hom.: 28327 Cov.: 32

Gnomad AFR AF: 0.611

Gnomad AMI AF: 0.581

Gnomad AMR AF: 0.555

Gnomad ASJ AF: 0.641

Gnomad EAS AF: 0.627

Gnomad SAS AF: 0.506

Gnomad FIN AF: 0.676

Gnomad MID AF: 0.510

Gnomad NFE AF: 0.617

Gnomad OTH AF: 0.579

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

GnomAD4 genome AF: 0.610 AC: 92741 AN: 152074 Hom.: 28355 Cov.: 32 AF XY: 0.609 AC XY: 45252 AN XY: 74338

African (AFR) AF: 0.612 AC: 25366 AN: 41446

American (AMR) AF: 0.555 AC: 8475 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.641 AC: 2223 AN: 3470

East Asian (EAS) AF: 0.625 AC: 3241 AN: 5184

South Asian (SAS) AF: 0.508 AC: 2452 AN: 4824

European-Finnish (FIN) AF: 0.676 AC: 7157 AN: 10586

Middle Eastern (MID) AF: 0.514 AC: 150 AN: 292

European-Non Finnish (NFE) AF: 0.617 AC: 41933 AN: 67978

Other (OTH) AF: 0.575 AC: 1215 AN: 2112

Alfa AF: 0.610 Hom.: 93868

Bravo AF: 0.608

Asia WGS AF: 0.563 AC: 1956 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.9
DANN	Benign	0.50
PhyloP100		-0.42

Splicing

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

Other links and lift over

dbSNP: rs13043330; hg19: chr20-3756597; COSMIC: COSV65729585;