20-49493651-C-T

Variant names:

• chr20-49493651-C-T
• rs6095541

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 0.204 in 152,168 control chromosomes in the GnomAD database, including 3,556 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 0.20 (3556 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.97
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.3 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: 0.204 AC: 31026 AN: 152048 Hom.: 3557 Cov.: 32

Gnomad AFR AF: 0.305

Gnomad AMI AF: 0.118

Gnomad AMR AF: 0.168

Gnomad ASJ AF: 0.207

Gnomad EAS AF: 0.0968

Gnomad SAS AF: 0.0933

Gnomad FIN AF: 0.118

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.180

Gnomad OTH AF: 0.226

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

GnomAD4 genome AF: 0.204 AC: 31030 AN: 152168 Hom.: 3556 Cov.: 32 AF XY: 0.200 AC XY: 14871 AN XY: 74396

African (AFR) AF: 0.305 AC: 12642 AN: 41492

American (AMR) AF: 0.168 AC: 2570 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.207 AC: 718 AN: 3472

East Asian (EAS) AF: 0.0966 AC: 501 AN: 5188

South Asian (SAS) AF: 0.0933 AC: 451 AN: 4832

European-Finnish (FIN) AF: 0.118 AC: 1246 AN: 10594

Middle Eastern (MID) AF: 0.194 AC: 57 AN: 294

European-Non Finnish (NFE) AF: 0.180 AC: 12264 AN: 67982

Other (OTH) AF: 0.224 AC: 473 AN: 2108

Alfa AF: 0.185 Hom.: 11356

Bravo AF: 0.210

Asia WGS AF: 0.133 AC: 462 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	0.14
DANN	Benign	0.16
PhyloP100		-3.0

Splicing

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

Other links and lift over

dbSNP: rs6095541; hg19: chr20-48110188;