10-124456270-C-T

Variant names:

• chr10-124456270-C-T
• rs908366

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 0.252 in 151,966 control chromosomes in the GnomAD database, including 5,773 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 0.25 (5773 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.198
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.381 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.252 AC: 38220 AN: 151850 Hom.: 5779 Cov.: 32

Gnomad AFR AF: 0.0889

Gnomad AMI AF: 0.410

Gnomad AMR AF: 0.281

Gnomad ASJ AF: 0.207

Gnomad EAS AF: 0.395

Gnomad SAS AF: 0.241

Gnomad FIN AF: 0.278

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.330

Gnomad OTH AF: 0.242

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

GnomAD4 genome AF: 0.252 AC: 38230 AN: 151966 Hom.: 5773 Cov.: 32 AF XY: 0.249 AC XY: 18523 AN XY: 74276

African (AFR) AF: 0.0889 AC: 3681 AN: 41408

American (AMR) AF: 0.281 AC: 4282 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.207 AC: 719 AN: 3472

East Asian (EAS) AF: 0.396 AC: 2042 AN: 5162

South Asian (SAS) AF: 0.240 AC: 1156 AN: 4824

European-Finnish (FIN) AF: 0.278 AC: 2932 AN: 10562

Middle Eastern (MID) AF: 0.248 AC: 73 AN: 294

European-Non Finnish (NFE) AF: 0.330 AC: 22463 AN: 67980

Other (OTH) AF: 0.242 AC: 510 AN: 2106

Alfa AF: 0.297 Hom.: 10404

Bravo AF: 0.245

Asia WGS AF: 0.234 AC: 813 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.1
DANN	Benign	0.58
PhyloP100		0.20

Splicing

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

Other links and lift over

dbSNP: rs908366; hg19: chr10-126144839; COSMIC: COSV64835486;