rs10893679

Variant names:

• chr11-127411484-G-A
• rs10893679

Your query was ambiguous. Multiple possible variants found:

• chr11-127411484-G-A
• chr11-127411484-G-C

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 0.137 in 152,212 control chromosomes in the GnomAD database, including 1,665 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 0.14 (1665 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.359

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.244 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: 0.137 AC: 20849 AN: 152094 Hom.: 1661 Cov.: 33

Gnomad AFR AF: 0.204

Gnomad AMI AF: 0.0164

Gnomad AMR AF: 0.0904

Gnomad ASJ AF: 0.146

Gnomad EAS AF: 0.167

Gnomad SAS AF: 0.257

Gnomad FIN AF: 0.102

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.102

Gnomad OTH AF: 0.144

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

GnomAD4 genome AF: 0.137 AC: 20859 AN: 152212 Hom.: 1665 Cov.: 33 AF XY: 0.138 AC XY: 10297 AN XY: 74424

Gnomad4 AFR AF: 0.204

Gnomad4 AMR AF: 0.0905

Gnomad4 ASJ AF: 0.146

Gnomad4 EAS AF: 0.166

Gnomad4 SAS AF: 0.256

Gnomad4 FIN AF: 0.102

Gnomad4 NFE AF: 0.102

Gnomad4 OTH AF: 0.146

Alfa AF: 0.0274 Hom.: 17

Bravo AF: 0.137

Asia WGS AF: 0.234 AC: 816 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.64
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10893679; hg19: chr11-127281379;