rs10830099

Variant names:

• chr10-127486101-C-T
• rs10830099

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 0.522 in 151,998 control chromosomes in the GnomAD database, including 21,368 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 0.52 (21368 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.476

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 = 0.581 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: 0.522 AC: 79320 AN: 151880 Hom.: 21354 Cov.: 32

Gnomad AFR AF: 0.396

Gnomad AMI AF: 0.534

Gnomad AMR AF: 0.571

Gnomad ASJ AF: 0.586

Gnomad EAS AF: 0.570

Gnomad SAS AF: 0.531

Gnomad FIN AF: 0.480

Gnomad MID AF: 0.592

Gnomad NFE AF: 0.586

Gnomad OTH AF: 0.535

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

GnomAD4 genome AF: 0.522 AC: 79379 AN: 151998 Hom.: 21368 Cov.: 32 AF XY: 0.517 AC XY: 38414 AN XY: 74302

Gnomad4 AFR AF: 0.396

Gnomad4 AMR AF: 0.572

Gnomad4 ASJ AF: 0.586

Gnomad4 EAS AF: 0.570

Gnomad4 SAS AF: 0.531

Gnomad4 FIN AF: 0.480

Gnomad4 NFE AF: 0.586

Gnomad4 OTH AF: 0.537

Alfa AF: 0.581 Hom.: 51991

Bravo AF: 0.523

Asia WGS AF: 0.569 AC: 1979 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	0.68
DANN	Benign	0.26

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10830099; hg19: chr10-129284365;