10-73886124-G-T

Variant names:

• chr10-73886124-G-T
• rs2633303

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 0.725 in 152,024 control chromosomes in the GnomAD database, including 40,685 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 0.73 (40685 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.332

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.766 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: 0.725 AC: 110194 AN: 151908 Hom.: 40652 Cov.: 31

Gnomad AFR AF: 0.773

Gnomad AMI AF: 0.687

Gnomad AMR AF: 0.598

Gnomad ASJ AF: 0.907

Gnomad EAS AF: 0.481

Gnomad SAS AF: 0.604

Gnomad FIN AF: 0.630

Gnomad MID AF: 0.861

Gnomad NFE AF: 0.756

Gnomad OTH AF: 0.777

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

GnomAD4 genome AF: 0.725 AC: 110262 AN: 152024 Hom.: 40685 Cov.: 31 AF XY: 0.716 AC XY: 53176 AN XY: 74312

Gnomad4 AFR AF: 0.773

Gnomad4 AMR AF: 0.597

Gnomad4 ASJ AF: 0.907

Gnomad4 EAS AF: 0.481

Gnomad4 SAS AF: 0.604

Gnomad4 FIN AF: 0.630

Gnomad4 NFE AF: 0.756

Gnomad4 OTH AF: 0.769

Alfa AF: 0.708 Hom.: 4870

Bravo AF: 0.726

Asia WGS AF: 0.523 AC: 1824 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	2.3
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2633303; hg19: chr10-75645882;