rs10049090

Variant names:

• chr3-157079913-G-A
• rs10049090

Your query was ambiguous. Multiple possible variants found:

• chr3-157079913-G-A
• chr3-157079913-G-C
• chr3-157079913-G-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 0.463 in 151,958 control chromosomes in the GnomAD database, including 16,782 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 0.46 (16782 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.836

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.627 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.463 AC: 70370 AN: 151840 Hom.: 16766 Cov.: 32

Gnomad AFR AF: 0.534

Gnomad AMI AF: 0.405

Gnomad AMR AF: 0.463

Gnomad ASJ AF: 0.554

Gnomad EAS AF: 0.645

Gnomad SAS AF: 0.527

Gnomad FIN AF: 0.328

Gnomad MID AF: 0.579

Gnomad NFE AF: 0.418

Gnomad OTH AF: 0.498

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

GnomAD4 genome AF: 0.463 AC: 70423 AN: 151958 Hom.: 16782 Cov.: 32 AF XY: 0.462 AC XY: 34290 AN XY: 74272

Gnomad4 AFR AF: 0.534

Gnomad4 AMR AF: 0.463

Gnomad4 ASJ AF: 0.554

Gnomad4 EAS AF: 0.646

Gnomad4 SAS AF: 0.525

Gnomad4 FIN AF: 0.328

Gnomad4 NFE AF: 0.418

Gnomad4 OTH AF: 0.495

Alfa AF: 0.451 Hom.: 2881

Bravo AF: 0.476

Asia WGS AF: 0.565 AC: 1966 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.50
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10049090; hg19: chr3-156797702;