chr10-121372531-T-C

Variant names:

• chr10-121372531-T-C
• rs10886927

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.314 in 151,990 control chromosomes in the GnomAD database, including 8,185 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 0.31 (8185 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.34
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.391 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: 0.314 AC: 47657 AN: 151872 Hom.: 8178 Cov.: 32

Gnomad AFR AF: 0.168

Gnomad AMI AF: 0.373

Gnomad AMR AF: 0.277

Gnomad ASJ AF: 0.393

Gnomad EAS AF: 0.330

Gnomad SAS AF: 0.291

Gnomad FIN AF: 0.383

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.395

Gnomad OTH AF: 0.330

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

GnomAD4 genome AF: 0.314 AC: 47685 AN: 151990 Hom.: 8185 Cov.: 32 AF XY: 0.313 AC XY: 23241 AN XY: 74268

African (AFR) AF: 0.169 AC: 7001 AN: 41444

American (AMR) AF: 0.277 AC: 4223 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.393 AC: 1363 AN: 3470

East Asian (EAS) AF: 0.329 AC: 1696 AN: 5154

South Asian (SAS) AF: 0.292 AC: 1404 AN: 4812

European-Finnish (FIN) AF: 0.383 AC: 4037 AN: 10550

Middle Eastern (MID) AF: 0.289 AC: 85 AN: 294

European-Non Finnish (NFE) AF: 0.395 AC: 26846 AN: 67974

Other (OTH) AF: 0.327 AC: 690 AN: 2108

Alfa AF: 0.367 Hom.: 18172

Bravo AF: 0.298

Asia WGS AF: 0.286 AC: 996 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.52
DANN	Benign	0.44
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs10886927; hg19: chr10-123132045;