10-73923832-C-T

Variant names:

• chr10-73923832-C-T
• rs2633314

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 0.492 in 152,088 control chromosomes in the GnomAD database, including 19,169 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 0.49 (19169 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0320

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.48).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.562 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: 0.492 AC: 74838 AN: 151970 Hom.: 19166 Cov.: 32

Gnomad AFR AF: 0.447

Gnomad AMI AF: 0.502

Gnomad AMR AF: 0.461

Gnomad ASJ AF: 0.587

Gnomad EAS AF: 0.119

Gnomad SAS AF: 0.293

Gnomad FIN AF: 0.464

Gnomad MID AF: 0.598

Gnomad NFE AF: 0.566

Gnomad OTH AF: 0.561

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

GnomAD4 genome AF: 0.492 AC: 74859 AN: 152088 Hom.: 19169 Cov.: 32 AF XY: 0.485 AC XY: 36038 AN XY: 74342

Gnomad4 AFR AF: 0.447

Gnomad4 AMR AF: 0.461

Gnomad4 ASJ AF: 0.587

Gnomad4 EAS AF: 0.119

Gnomad4 SAS AF: 0.294

Gnomad4 FIN AF: 0.464

Gnomad4 NFE AF: 0.566

Gnomad4 OTH AF: 0.557

Alfa AF: 0.513 Hom.: 2496

Bravo AF: 0.493

Asia WGS AF: 0.207 AC: 722 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.48
CADD	Benign	6.3
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2633314; hg19: chr10-75683590;