10-127486101-C-T

Variant names:

• chr10-127486101-C-T
• rs10830099

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 0.522 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
• Publications: 3 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 = 0.581 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.396 AC: 16416 AN: 41448

American (AMR) AF: 0.572 AC: 8740 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.586 AC: 2031 AN: 3466

East Asian (EAS) AF: 0.570 AC: 2939 AN: 5158

South Asian (SAS) AF: 0.531 AC: 2562 AN: 4824

European-Finnish (FIN) AF: 0.480 AC: 5063 AN: 10550

Middle Eastern (MID) AF: 0.582 AC: 171 AN: 294

European-Non Finnish (NFE) AF: 0.586 AC: 39842 AN: 67954

Other (OTH) AF: 0.537 AC: 1131 AN: 2106

Alfa AF: 0.568 Hom.: 76909

Bravo AF: 0.523

Asia WGS AF: 0.569 AC: 1979 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.68
DANN	Benign	0.26
PhyloP100		-0.48

Splicing

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

Other links and lift over

dbSNP: rs10830099; hg19: chr10-129284365;