rs10049088

Variant names:

• chr3-157079859-C-T
• rs10049088

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 0.357 in 151,734 control chromosomes in the GnomAD database, including 10,159 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 0.36 (10159 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.444

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.487 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: 0.358 AC: 54205 AN: 151616 Hom.: 10163 Cov.: 31

Gnomad AFR AF: 0.255

Gnomad AMI AF: 0.404

Gnomad AMR AF: 0.414

Gnomad ASJ AF: 0.501

Gnomad EAS AF: 0.504

Gnomad SAS AF: 0.257

Gnomad FIN AF: 0.309

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.401

Gnomad OTH AF: 0.401

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

GnomAD4 genome AF: 0.357 AC: 54220 AN: 151734 Hom.: 10159 Cov.: 31 AF XY: 0.354 AC XY: 26201 AN XY: 74110

Gnomad4 AFR AF: 0.255

Gnomad4 AMR AF: 0.414

Gnomad4 ASJ AF: 0.501

Gnomad4 EAS AF: 0.503

Gnomad4 SAS AF: 0.257

Gnomad4 FIN AF: 0.309

Gnomad4 NFE AF: 0.401

Gnomad4 OTH AF: 0.399

Alfa AF: 0.384 Hom.: 1921

Bravo AF: 0.364

Asia WGS AF: 0.354 AC: 1228 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	6.8
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10049088; hg19: chr3-156797648;