rs10508349

chr10-8257001-G-Achr10-8257001-G-Cchr10-8257001-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 0.0507 in 152,250 control chromosomes in the GnomAD database, including 1,143 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 0.051 (1143 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.539

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.472 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: 0.0507 AC: 7710 AN: 152132 Hom.: 1136 Cov.: 32

Gnomad AFR AF: 0.0193

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.202

Gnomad ASJ AF: 0.0150

Gnomad EAS AF: 0.488

Gnomad SAS AF: 0.0833

Gnomad FIN AF: 0.0444

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.00376

Gnomad OTH AF: 0.0549

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

GnomAD4 genome AF: 0.0507 AC: 7724 AN: 152250 Hom.: 1143 Cov.: 32 AF XY: 0.0573 AC XY: 4265 AN XY: 74446

Gnomad4 AFR AF: 0.0193

Gnomad4 AMR AF: 0.203

Gnomad4 ASJ AF: 0.0150

Gnomad4 EAS AF: 0.487

Gnomad4 SAS AF: 0.0844

Gnomad4 FIN AF: 0.0444

Gnomad4 NFE AF: 0.00376

Gnomad4 OTH AF: 0.0548

Alfa AF: 0.0614 Hom.: 255

Bravo AF: 0.0684

Asia WGS AF: 0.225 AC: 781 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.098
Dann	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10508349; hg19: chr10-8298964;