rs2633298

chr10-73906581-C-Gchr10-73906581-C-T

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 0.649 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.600

Gnomad4 AMR AF: 0.561

Gnomad4 ASJ AF: 0.848

Gnomad4 EAS AF: 0.374

Gnomad4 SAS AF: 0.548

Gnomad4 FIN AF: 0.604

Gnomad4 NFE AF: 0.720

Gnomad4 OTH AF: 0.690

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2633298; hg19: chr10-75666339;