rs10490827

Positions:

• chr3-144552616-C-T

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

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

Gnomad4 AFR AF: 0.0158

Gnomad4 AMR AF: 0.0865

Gnomad4 ASJ AF: 0.132

Gnomad4 EAS AF: 0.263

Gnomad4 SAS AF: 0.155

Gnomad4 FIN AF: 0.0474

Gnomad4 NFE AF: 0.0794

Gnomad4 OTH AF: 0.0853

Alfa AF: 0.0828 Hom.: 270

Bravo AF: 0.0705

Asia WGS AF: 0.220 AC: 762 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10490827; hg19: chr3-144271458;