rs734241

chr10-113479843-G-Achr10-113479843-G-Cchr10-113479843-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 0.115 in 152,170 control chromosomes in the GnomAD database, including 2,084 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 0.12 (2084 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.684

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.382 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: 0.115 AC: 17522 AN: 152050 Hom.: 2064 Cov.: 33

Gnomad AFR AF: 0.0516

Gnomad AMI AF: 0.00658

Gnomad AMR AF: 0.338

Gnomad ASJ AF: 0.109

Gnomad EAS AF: 0.397

Gnomad SAS AF: 0.319

Gnomad FIN AF: 0.132

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.0669

Gnomad OTH AF: 0.132

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

GnomAD4 genome AF: 0.115 AC: 17561 AN: 152170 Hom.: 2084 Cov.: 33 AF XY: 0.128 AC XY: 9522 AN XY: 74382

Gnomad4 AFR AF: 0.0516

Gnomad4 AMR AF: 0.339

Gnomad4 ASJ AF: 0.109

Gnomad4 EAS AF: 0.397

Gnomad4 SAS AF: 0.319

Gnomad4 FIN AF: 0.132

Gnomad4 NFE AF: 0.0669

Gnomad4 OTH AF: 0.135

Alfa AF: 0.0815 Hom.: 1792

Bravo AF: 0.129

Asia WGS AF: 0.361 AC: 1254 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	5.5
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: rs734241; hg19: chr10-115239602;