rs10905651

Positions:

• chr10-10031581-G-A

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 0.535 in 152,012 control chromosomes in the GnomAD database, including 22,291 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 0.53 (22291 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.567

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.649 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.535 AC: 81226 AN: 151894 Hom.: 22270 Cov.: 32

Gnomad AFR AF: 0.655

Gnomad AMI AF: 0.436

Gnomad AMR AF: 0.517

Gnomad ASJ AF: 0.512

Gnomad EAS AF: 0.399

Gnomad SAS AF: 0.376

Gnomad FIN AF: 0.397

Gnomad MID AF: 0.579

Gnomad NFE AF: 0.510

Gnomad OTH AF: 0.543

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

GnomAD4 genome AF: 0.535 AC: 81288 AN: 152012 Hom.: 22291 Cov.: 32 AF XY: 0.527 AC XY: 39128 AN XY: 74278

Gnomad4 AFR AF: 0.655

Gnomad4 AMR AF: 0.517

Gnomad4 ASJ AF: 0.512

Gnomad4 EAS AF: 0.400

Gnomad4 SAS AF: 0.375

Gnomad4 FIN AF: 0.397

Gnomad4 NFE AF: 0.510

Gnomad4 OTH AF: 0.536

Alfa AF: 0.510 Hom.: 9310

Bravo AF: 0.555

Asia WGS AF: 0.381 AC: 1327 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.79
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10905651; hg19: chr10-10073544;