rs2633298

Variant names:

• chr10-73906581-C-G
• rs2633298

Your query was ambiguous. Multiple possible variants found:

• chr10-73906581-C-G
• chr10-73906581-C-T

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 0.649 in 152,094 control chromosomes in the GnomAD database, including 32,665 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 0.65 (32665 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0180
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.715 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: 0.649 AC: 98637 AN: 151976 Hom.: 32655 Cov.: 32

Gnomad AFR AF: 0.601

Gnomad AMI AF: 0.683

Gnomad AMR AF: 0.562

Gnomad ASJ AF: 0.848

Gnomad EAS AF: 0.373

Gnomad SAS AF: 0.548

Gnomad FIN AF: 0.604

Gnomad MID AF: 0.759

Gnomad NFE AF: 0.720

Gnomad OTH AF: 0.697

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

GnomAD4 genome AF: 0.649 AC: 98669 AN: 152094 Hom.: 32665 Cov.: 32 AF XY: 0.641 AC XY: 47627 AN XY: 74348

African (AFR) AF: 0.600 AC: 24899 AN: 41466

American (AMR) AF: 0.561 AC: 8580 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.848 AC: 2942 AN: 3470

East Asian (EAS) AF: 0.374 AC: 1933 AN: 5170

South Asian (SAS) AF: 0.548 AC: 2648 AN: 4828

European-Finnish (FIN) AF: 0.604 AC: 6381 AN: 10570

Middle Eastern (MID) AF: 0.765 AC: 225 AN: 294

European-Non Finnish (NFE) AF: 0.720 AC: 48986 AN: 67994

Other (OTH) AF: 0.690 AC: 1455 AN: 2110

Alfa AF: 0.666 Hom.: 3996

Bravo AF: 0.647

Asia WGS AF: 0.434 AC: 1510 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	6.7
DANN	Benign	0.78
PhyloP100		0.018

Splicing

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

Other links and lift over

dbSNP: rs2633298; hg19: chr10-75666339;