chr10-122927140-T-C

Variant names:

• chr10-122927140-T-C
• rs10794579

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 0.535 in 152,024 control chromosomes in the GnomAD database, including 22,153 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 (22153 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.46
• Publications: 22 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.571 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: 0.535 AC: 81294 AN: 151906 Hom.: 22154 Cov.: 32

Gnomad AFR AF: 0.450

Gnomad AMI AF: 0.749

Gnomad AMR AF: 0.514

Gnomad ASJ AF: 0.525

Gnomad EAS AF: 0.522

Gnomad SAS AF: 0.512

Gnomad FIN AF: 0.635

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.576

Gnomad OTH AF: 0.542

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

GnomAD4 genome AF: 0.535 AC: 81324 AN: 152024 Hom.: 22153 Cov.: 32 AF XY: 0.536 AC XY: 39813 AN XY: 74306

African (AFR) AF: 0.450 AC: 18651 AN: 41470

American (AMR) AF: 0.514 AC: 7855 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.525 AC: 1822 AN: 3468

East Asian (EAS) AF: 0.524 AC: 2710 AN: 5168

South Asian (SAS) AF: 0.511 AC: 2464 AN: 4818

European-Finnish (FIN) AF: 0.635 AC: 6707 AN: 10562

Middle Eastern (MID) AF: 0.483 AC: 142 AN: 294

European-Non Finnish (NFE) AF: 0.576 AC: 39153 AN: 67942

Other (OTH) AF: 0.539 AC: 1138 AN: 2110

Alfa AF: 0.561 Hom.: 37109

Bravo AF: 0.520

Asia WGS AF: 0.503 AC: 1750 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.22
DANN	Benign	0.39
PhyloP100		-2.5

Splicing

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

Other links and lift over

dbSNP: rs10794579; hg19: chr10-124686656;