rs10740308

Positions:

• chr10-68695139-A-C
• chr10-68695139-A-G
• chr10-68695139-A-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 0.776 in 152,036 control chromosomes in the GnomAD database, including 46,168 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 0.78 (46168 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.83

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.72).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.822 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: 0.776 AC: 117889 AN: 151918 Hom.: 46150 Cov.: 32

Gnomad AFR AF: 0.665

Gnomad AMI AF: 0.911

Gnomad AMR AF: 0.782

Gnomad ASJ AF: 0.867

Gnomad EAS AF: 0.843

Gnomad SAS AF: 0.769

Gnomad FIN AF: 0.804

Gnomad MID AF: 0.820

Gnomad NFE AF: 0.826

Gnomad OTH AF: 0.796

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

GnomAD4 genome AF: 0.776 AC: 117951 AN: 152036 Hom.: 46168 Cov.: 32 AF XY: 0.775 AC XY: 57581 AN XY: 74298

Gnomad4 AFR AF: 0.665

Gnomad4 AMR AF: 0.781

Gnomad4 ASJ AF: 0.867

Gnomad4 EAS AF: 0.842

Gnomad4 SAS AF: 0.770

Gnomad4 FIN AF: 0.804

Gnomad4 NFE AF: 0.826

Gnomad4 OTH AF: 0.796

Alfa AF: 0.815 Hom.: 45493

Bravo AF: 0.769

Asia WGS AF: 0.758 AC: 2635 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	8.0
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10740308; hg19: chr10-70454896;