rs10795733

chr10-6001515-C-Achr10-6001515-C-Gchr10-6001515-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 0.417 in 151,792 control chromosomes in the GnomAD database, including 14,131 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 0.42 (14131 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.50

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 (NFE) allele frequency at 95% confidence interval = 0.501 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: 0.417 AC: 63295 AN: 151674 Hom.: 14124 Cov.: 30

Gnomad AFR AF: 0.280

Gnomad AMI AF: 0.719

Gnomad AMR AF: 0.388

Gnomad ASJ AF: 0.478

Gnomad EAS AF: 0.390

Gnomad SAS AF: 0.421

Gnomad FIN AF: 0.393

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.506

Gnomad OTH AF: 0.420

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

GnomAD4 genome AF: 0.417 AC: 63340 AN: 151792 Hom.: 14131 Cov.: 30 AF XY: 0.410 AC XY: 30428 AN XY: 74162

Gnomad4 AFR AF: 0.281

Gnomad4 AMR AF: 0.387

Gnomad4 ASJ AF: 0.478

Gnomad4 EAS AF: 0.389

Gnomad4 SAS AF: 0.419

Gnomad4 FIN AF: 0.393

Gnomad4 NFE AF: 0.506

Gnomad4 OTH AF: 0.423

Alfa AF: 0.464 Hom.: 12021

Bravo AF: 0.409

Asia WGS AF: 0.447 AC: 1553 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	0.41
Dann	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10795733; hg19: chr10-6043478;