chr10-120415050-C-T

Variant names:

• chr10-120415050-C-T
• rs7916482

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 0.334 in 151,626 control chromosomes in the GnomAD database, including 11,646 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 0.33 (11646 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.193
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.646 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: 0.334 AC: 50539 AN: 151512 Hom.: 11610 Cov.: 30

Gnomad AFR AF: 0.652

Gnomad AMI AF: 0.162

Gnomad AMR AF: 0.180

Gnomad ASJ AF: 0.166

Gnomad EAS AF: 0.326

Gnomad SAS AF: 0.256

Gnomad FIN AF: 0.342

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.193

Gnomad OTH AF: 0.269

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

GnomAD4 genome AF: 0.334 AC: 50631 AN: 151626 Hom.: 11646 Cov.: 30 AF XY: 0.336 AC XY: 24917 AN XY: 74052

African (AFR) AF: 0.653 AC: 26947 AN: 41286

American (AMR) AF: 0.180 AC: 2746 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.166 AC: 578 AN: 3472

East Asian (EAS) AF: 0.326 AC: 1669 AN: 5118

South Asian (SAS) AF: 0.255 AC: 1222 AN: 4796

European-Finnish (FIN) AF: 0.342 AC: 3577 AN: 10456

Middle Eastern (MID) AF: 0.180 AC: 53 AN: 294

European-Non Finnish (NFE) AF: 0.193 AC: 13121 AN: 67920

Other (OTH) AF: 0.271 AC: 571 AN: 2110

Alfa AF: 0.219 Hom.: 7984

Bravo AF: 0.335

Asia WGS AF: 0.339 AC: 1182 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.79
DANN	Benign	0.73
PhyloP100		-0.19

Splicing

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

Other links and lift over

dbSNP: rs7916482; hg19: chr10-122174562;