rs10490827

Variant names:

• chr3-144552616-C-T
• rs10490827

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 0.0706 in 152,192 control chromosomes in the GnomAD database, including 589 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 0.071 (589 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.957
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.252 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.0706 AC: 10737 AN: 152074 Hom.: 588 Cov.: 32

Gnomad AFR AF: 0.0158

Gnomad AMI AF: 0.0932

Gnomad AMR AF: 0.0866

Gnomad ASJ AF: 0.132

Gnomad EAS AF: 0.263

Gnomad SAS AF: 0.154

Gnomad FIN AF: 0.0474

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.0795

Gnomad OTH AF: 0.0848

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

GnomAD4 genome AF: 0.0706 AC: 10739 AN: 152192 Hom.: 589 Cov.: 32 AF XY: 0.0720 AC XY: 5359 AN XY: 74398

African (AFR) AF: 0.0158 AC: 655 AN: 41552

American (AMR) AF: 0.0865 AC: 1323 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.132 AC: 457 AN: 3472

East Asian (EAS) AF: 0.263 AC: 1360 AN: 5168

South Asian (SAS) AF: 0.155 AC: 749 AN: 4818

European-Finnish (FIN) AF: 0.0474 AC: 502 AN: 10594

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.0794 AC: 5400 AN: 67986

Other (OTH) AF: 0.0853 AC: 180 AN: 2110

Alfa AF: 0.0814 Hom.: 303

Bravo AF: 0.0705

Asia WGS AF: 0.220 AC: 762 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.089
DANN	Benign	0.43
PhyloP100		-0.96

Splicing

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

Other links and lift over

dbSNP: rs10490827; hg19: chr3-144271458;