rs11256313

chr10-6008329-G-A

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 0.111 in 152,072 control chromosomes in the GnomAD database, including 1,077 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 0.11 (1077 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.252

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.225 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: 0.110 AC: 16790 AN: 151954 Hom.: 1071 Cov.: 32

Gnomad AFR AF: 0.102

Gnomad AMI AF: 0.0800

Gnomad AMR AF: 0.143

Gnomad ASJ AF: 0.0963

Gnomad EAS AF: 0.237

Gnomad SAS AF: 0.118

Gnomad FIN AF: 0.124

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0977

Gnomad OTH AF: 0.0946

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

GnomAD4 genome AF: 0.111 AC: 16822 AN: 152072 Hom.: 1077 Cov.: 32 AF XY: 0.113 AC XY: 8412 AN XY: 74322

Gnomad4 AFR AF: 0.103

Gnomad4 AMR AF: 0.143

Gnomad4 ASJ AF: 0.0963

Gnomad4 EAS AF: 0.236

Gnomad4 SAS AF: 0.118

Gnomad4 FIN AF: 0.124

Gnomad4 NFE AF: 0.0977

Gnomad4 OTH AF: 0.0998

Alfa AF: 0.106 Hom.: 109

Bravo AF: 0.109

Asia WGS AF: 0.203 AC: 704 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	2.9
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: rs11256313; hg19: chr10-6050292; COSMIC: COSV56920084;