rs2633317

Variant names:

• chr10-73930510-A-G
• rs2633317

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 0.506 in 152,106 control chromosomes in the GnomAD database, including 20,249 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 0.51 (20249 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.590
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.578 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: 0.506 AC: 76968 AN: 151986 Hom.: 20245 Cov.: 33

Gnomad AFR AF: 0.458

Gnomad AMI AF: 0.503

Gnomad AMR AF: 0.471

Gnomad ASJ AF: 0.613

Gnomad EAS AF: 0.131

Gnomad SAS AF: 0.324

Gnomad FIN AF: 0.470

Gnomad MID AF: 0.687

Gnomad NFE AF: 0.583

Gnomad OTH AF: 0.580

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

GnomAD4 genome AF: 0.506 AC: 76998 AN: 152106 Hom.: 20249 Cov.: 33 AF XY: 0.498 AC XY: 37039 AN XY: 74348

African (AFR) AF: 0.458 AC: 18980 AN: 41470

American (AMR) AF: 0.470 AC: 7188 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.613 AC: 2128 AN: 3470

East Asian (EAS) AF: 0.131 AC: 679 AN: 5184

South Asian (SAS) AF: 0.324 AC: 1567 AN: 4832

European-Finnish (FIN) AF: 0.470 AC: 4976 AN: 10576

Middle Eastern (MID) AF: 0.680 AC: 200 AN: 294

European-Non Finnish (NFE) AF: 0.583 AC: 39611 AN: 67968

Other (OTH) AF: 0.575 AC: 1210 AN: 2106

Alfa AF: 0.534 Hom.: 2806

Bravo AF: 0.506

Asia WGS AF: 0.226 AC: 787 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.96
DANN	Benign	0.34
PhyloP100		-0.59

Splicing

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

Other links and lift over

dbSNP: rs2633317; hg19: chr10-75690268;