rs2633313

Positions:

• chr10-73924107-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 0.539 in 152,060 control chromosomes in the GnomAD database, including 22,921 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 0.54 (22921 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.41

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.578 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.539 AC: 81867 AN: 151942 Hom.: 22905 Cov.: 31

Gnomad AFR AF: 0.584

Gnomad AMI AF: 0.503

Gnomad AMR AF: 0.484

Gnomad ASJ AF: 0.605

Gnomad EAS AF: 0.118

Gnomad SAS AF: 0.318

Gnomad FIN AF: 0.468

Gnomad MID AF: 0.661

Gnomad NFE AF: 0.577

Gnomad OTH AF: 0.596

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

GnomAD4 genome AF: 0.539 AC: 81921 AN: 152060 Hom.: 22921 Cov.: 31 AF XY: 0.530 AC XY: 39391 AN XY: 74308

Gnomad4 AFR AF: 0.584

Gnomad4 AMR AF: 0.483

Gnomad4 ASJ AF: 0.605

Gnomad4 EAS AF: 0.118

Gnomad4 SAS AF: 0.317

Gnomad4 FIN AF: 0.468

Gnomad4 NFE AF: 0.577

Gnomad4 OTH AF: 0.590

Alfa AF: 0.550 Hom.: 2866

Bravo AF: 0.544

Asia WGS AF: 0.228 AC: 794 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.9
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2633313; hg19: chr10-75683865;