10-121372531-T-C

Position:

• chr10-121372531-T-C

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 0.314 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.169

Gnomad4 AMR AF: 0.277

Gnomad4 ASJ AF: 0.393

Gnomad4 EAS AF: 0.329

Gnomad4 SAS AF: 0.292

Gnomad4 FIN AF: 0.383

Gnomad4 NFE AF: 0.395

Gnomad4 OTH AF: 0.327

Alfa AF: 0.376 Hom.: 15088

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10886927; hg19: chr10-123132045;