rs4963452

Variant names:

• chr11-62048331-T-C
• rs4963452

Your query was ambiguous. Multiple possible variants found:

• chr11-62048331-T-C
• chr11-62048331-T-G

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 0.201 in 152,036 control chromosomes in the GnomAD database, including 3,794 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 (3794 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0200
• Publications: 15 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.405 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: 0.201 AC: 30500 AN: 151918 Hom.: 3783 Cov.: 32

Gnomad AFR AF: 0.160

Gnomad AMI AF: 0.188

Gnomad AMR AF: 0.406

Gnomad ASJ AF: 0.136

Gnomad EAS AF: 0.420

Gnomad SAS AF: 0.323

Gnomad FIN AF: 0.193

Gnomad MID AF: 0.197

Gnomad NFE AF: 0.158

Gnomad OTH AF: 0.214

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

GnomAD4 genome AF: 0.201 AC: 30535 AN: 152036 Hom.: 3794 Cov.: 32 AF XY: 0.209 AC XY: 15525 AN XY: 74322

African (AFR) AF: 0.160 AC: 6647 AN: 41488

American (AMR) AF: 0.407 AC: 6212 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.136 AC: 470 AN: 3460

East Asian (EAS) AF: 0.419 AC: 2164 AN: 5162

South Asian (SAS) AF: 0.322 AC: 1555 AN: 4824

European-Finnish (FIN) AF: 0.193 AC: 2043 AN: 10574

Middle Eastern (MID) AF: 0.199 AC: 58 AN: 292

European-Non Finnish (NFE) AF: 0.158 AC: 10761 AN: 67958

Other (OTH) AF: 0.216 AC: 454 AN: 2106

Alfa AF: 0.177 Hom.: 5063

Bravo AF: 0.215

Asia WGS AF: 0.408 AC: 1416 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	6.9
DANN	Benign	0.91
PhyloP100		0.020

Splicing

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

Other links and lift over

dbSNP: rs4963452; hg19: chr11-61815803;