10-16257952-C-T

Variant names:

• chr10-16257952-C-T
• rs10508503

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 0.0611 in 152,136 control chromosomes in the GnomAD database, including 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 0.061 (368 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.128
• Publications: 55 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0897 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: 0.0612 AC: 9303 AN: 152018 Hom.: 368 Cov.: 32

Gnomad AFR AF: 0.0145

Gnomad AMI AF: 0.0998

Gnomad AMR AF: 0.0558

Gnomad ASJ AF: 0.0916

Gnomad EAS AF: 0.00116

Gnomad SAS AF: 0.0187

Gnomad FIN AF: 0.0921

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0916

Gnomad OTH AF: 0.0622

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

GnomAD4 genome AF: 0.0611 AC: 9299 AN: 152136 Hom.: 368 Cov.: 32 AF XY: 0.0598 AC XY: 4448 AN XY: 74348

African (AFR) AF: 0.0145 AC: 601 AN: 41530

American (AMR) AF: 0.0558 AC: 852 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.0916 AC: 318 AN: 3472

East Asian (EAS) AF: 0.000967 AC: 5 AN: 5172

South Asian (SAS) AF: 0.0183 AC: 88 AN: 4818

European-Finnish (FIN) AF: 0.0921 AC: 974 AN: 10574

Middle Eastern (MID) AF: 0.0374 AC: 11 AN: 294

European-Non Finnish (NFE) AF: 0.0916 AC: 6229 AN: 67976

Other (OTH) AF: 0.0616 AC: 130 AN: 2112

Alfa AF: 0.0759 Hom.: 1424

Bravo AF: 0.0567

Asia WGS AF: 0.0130 AC: 44 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.1
DANN	Benign	0.73
PhyloP100		-0.13

Splicing

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

Other links and lift over

dbSNP: rs10508503; hg19: chr10-16299951;