chr3-122649500-C-T

Variant names:

• chr3-122649500-C-T
• rs2650951

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 0.123 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
• Publications: 10 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.283 AC: 11735 AN: 41458

American (AMR) AF: 0.0788 AC: 1204 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0822 AC: 285 AN: 3468

East Asian (EAS) AF: 0.0187 AC: 97 AN: 5180

South Asian (SAS) AF: 0.0617 AC: 297 AN: 4812

European-Finnish (FIN) AF: 0.0437 AC: 461 AN: 10560

Middle Eastern (MID) AF: 0.139 AC: 41 AN: 294

European-Non Finnish (NFE) AF: 0.0635 AC: 4315 AN: 67984

Other (OTH) AF: 0.128 AC: 270 AN: 2112

Alfa AF: 0.0812 Hom.: 2674

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
PhyloP100		0.12

Splicing

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

Other links and lift over

dbSNP: rs2650951; hg19: chr3-122368347;