chr20-49496763-T-C

Variant names:

• chr20-49496763-T-C
• rs6095543

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 0.149 in 152,144 control chromosomes in the GnomAD database, including 1,737 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 0.15 (1737 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0180
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.71).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.185 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

Frequencies

GnomAD3 genomes AF: 0.149 AC: 22608 AN: 152026 Hom.: 1740 Cov.: 32

Gnomad AFR AF: 0.119

Gnomad AMI AF: 0.118

Gnomad AMR AF: 0.148

Gnomad ASJ AF: 0.202

Gnomad EAS AF: 0.195

Gnomad SAS AF: 0.106

Gnomad FIN AF: 0.104

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.170

Gnomad OTH AF: 0.193

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

GnomAD4 genome AF: 0.149 AC: 22595 AN: 152144 Hom.: 1737 Cov.: 32 AF XY: 0.147 AC XY: 10962 AN XY: 74386

African (AFR) AF: 0.119 AC: 4923 AN: 41528

American (AMR) AF: 0.148 AC: 2266 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.202 AC: 699 AN: 3464

East Asian (EAS) AF: 0.195 AC: 1009 AN: 5180

South Asian (SAS) AF: 0.105 AC: 506 AN: 4810

European-Finnish (FIN) AF: 0.104 AC: 1101 AN: 10604

Middle Eastern (MID) AF: 0.180 AC: 53 AN: 294

European-Non Finnish (NFE) AF: 0.170 AC: 11527 AN: 67960

Other (OTH) AF: 0.192 AC: 404 AN: 2108

Alfa AF: 0.169 Hom.: 2604

Bravo AF: 0.150

Asia WGS AF: 0.163 AC: 566 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	9.4
DANN	Benign	0.83
PhyloP100		-0.018

Splicing

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

Other links and lift over

dbSNP: rs6095543; hg19: chr20-48113300;