rs1035209

Variant names:

• chr10-99585609-C-T
• rs1035209

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 0.146 in 152,242 control chromosomes in the GnomAD database, including 1,779 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 0.15 (1779 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.137
• Publications: 46 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.187 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: 0.146 AC: 22163 AN: 152124 Hom.: 1776 Cov.: 32

Gnomad AFR AF: 0.0869

Gnomad AMI AF: 0.137

Gnomad AMR AF: 0.111

Gnomad ASJ AF: 0.137

Gnomad EAS AF: 0.175

Gnomad SAS AF: 0.103

Gnomad FIN AF: 0.155

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.190

Gnomad OTH AF: 0.132

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

GnomAD4 genome AF: 0.146 AC: 22180 AN: 152242 Hom.: 1779 Cov.: 32 AF XY: 0.142 AC XY: 10600 AN XY: 74436

African (AFR) AF: 0.0870 AC: 3617 AN: 41560

American (AMR) AF: 0.111 AC: 1698 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.137 AC: 475 AN: 3470

East Asian (EAS) AF: 0.175 AC: 905 AN: 5166

South Asian (SAS) AF: 0.103 AC: 500 AN: 4834

European-Finnish (FIN) AF: 0.155 AC: 1640 AN: 10594

Middle Eastern (MID) AF: 0.0918 AC: 27 AN: 294

European-Non Finnish (NFE) AF: 0.190 AC: 12917 AN: 68008

Other (OTH) AF: 0.131 AC: 276 AN: 2110

Alfa AF: 0.171 Hom.: 9695

Bravo AF: 0.139

Asia WGS AF: 0.129 AC: 450 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	5.4
DANN	Benign	0.57
PhyloP100		0.14

Splicing

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

Other links and lift over

dbSNP: rs1035209; hg19: chr10-101345366;