chr10-73924107-C-T

Variant names:

• chr10-73924107-C-T
• rs2633313

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 0.539 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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.584 AC: 24207 AN: 41468

American (AMR) AF: 0.483 AC: 7382 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.605 AC: 2094 AN: 3462

East Asian (EAS) AF: 0.118 AC: 610 AN: 5170

South Asian (SAS) AF: 0.317 AC: 1530 AN: 4824

European-Finnish (FIN) AF: 0.468 AC: 4951 AN: 10570

Middle Eastern (MID) AF: 0.656 AC: 193 AN: 294

European-Non Finnish (NFE) AF: 0.577 AC: 39247 AN: 67968

Other (OTH) AF: 0.590 AC: 1248 AN: 2114

Alfa AF: 0.550 Hom.: 2994

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
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs2633313; hg19: chr10-75683865;