10-102640376-C-T

Variant names:

• chr10-102640376-C-T
• rs10883757

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 0.137 in 152,136 control chromosomes in the GnomAD database, including 1,829 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 0.14 (1829 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.458
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.399 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: 0.137 AC: 20757 AN: 152018 Hom.: 1824 Cov.: 32

Gnomad AFR AF: 0.167

Gnomad AMI AF: 0.122

Gnomad AMR AF: 0.191

Gnomad ASJ AF: 0.0637

Gnomad EAS AF: 0.413

Gnomad SAS AF: 0.220

Gnomad FIN AF: 0.0719

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0929

Gnomad OTH AF: 0.150

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

GnomAD4 genome AF: 0.137 AC: 20797 AN: 152136 Hom.: 1829 Cov.: 32 AF XY: 0.140 AC XY: 10442 AN XY: 74402

African (AFR) AF: 0.167 AC: 6914 AN: 41502

American (AMR) AF: 0.191 AC: 2920 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.0637 AC: 221 AN: 3470

East Asian (EAS) AF: 0.413 AC: 2136 AN: 5168

South Asian (SAS) AF: 0.221 AC: 1068 AN: 4822

European-Finnish (FIN) AF: 0.0719 AC: 762 AN: 10596

Middle Eastern (MID) AF: 0.0748 AC: 22 AN: 294

European-Non Finnish (NFE) AF: 0.0929 AC: 6319 AN: 67998

Other (OTH) AF: 0.154 AC: 324 AN: 2110

Alfa AF: 0.126 Hom.: 636

Bravo AF: 0.149

Asia WGS AF: 0.310 AC: 1073 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	5.7
DANN	Benign	0.66
PhyloP100		0.46

Splicing

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

Other links and lift over

dbSNP: rs10883757; hg19: chr10-104400133;