rs2650951

Variant names:

• chr3-122649500-C-T
• rs2650951

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.123 in 152,062 control chromosomes in the GnomAD database, including 1,966 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 0.12 (1966 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.121

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.279 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: 0.123 AC: 18703 AN: 151944 Hom.: 1960 Cov.: 32

Gnomad AFR AF: 0.283

Gnomad AMI AF: 0.0407

Gnomad AMR AF: 0.0789

Gnomad ASJ AF: 0.0822

Gnomad EAS AF: 0.0185

Gnomad SAS AF: 0.0606

Gnomad FIN AF: 0.0437

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.0635

Gnomad OTH AF: 0.129

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

GnomAD4 genome AF: 0.123 AC: 18742 AN: 152062 Hom.: 1966 Cov.: 32 AF XY: 0.119 AC XY: 8869 AN XY: 74340

Gnomad4 AFR AF: 0.283

Gnomad4 AMR AF: 0.0788

Gnomad4 ASJ AF: 0.0822

Gnomad4 EAS AF: 0.0187

Gnomad4 SAS AF: 0.0617

Gnomad4 FIN AF: 0.0437

Gnomad4 NFE AF: 0.0635

Gnomad4 OTH AF: 0.128

Alfa AF: 0.0697 Hom.: 710

Bravo AF: 0.134

Asia WGS AF: 0.0640 AC: 221 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	3.2
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2650951; hg19: chr3-122368347;