11-134868376-A-C

Variant names:

• chr11-134868376-A-C
• rs906628

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.0996 in 152,052 control chromosomes in the GnomAD database, including 1,051 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 0.10 (1051 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.43
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.2 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.0996 AC: 15131 AN: 151934 Hom.: 1050 Cov.: 31

Gnomad AFR AF: 0.204

Gnomad AMI AF: 0.101

Gnomad AMR AF: 0.0588

Gnomad ASJ AF: 0.0799

Gnomad EAS AF: 0.0296

Gnomad SAS AF: 0.0364

Gnomad FIN AF: 0.0386

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.0657

Gnomad OTH AF: 0.0949

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

GnomAD4 genome AF: 0.0996 AC: 15145 AN: 152052 Hom.: 1051 Cov.: 31 AF XY: 0.0966 AC XY: 7186 AN XY: 74352

African (AFR) AF: 0.204 AC: 8444 AN: 41430

American (AMR) AF: 0.0587 AC: 897 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.0799 AC: 277 AN: 3466

East Asian (EAS) AF: 0.0297 AC: 153 AN: 5158

South Asian (SAS) AF: 0.0364 AC: 175 AN: 4806

European-Finnish (FIN) AF: 0.0386 AC: 409 AN: 10608

Middle Eastern (MID) AF: 0.112 AC: 33 AN: 294

European-Non Finnish (NFE) AF: 0.0657 AC: 4467 AN: 67996

Other (OTH) AF: 0.0939 AC: 198 AN: 2108

Alfa AF: 0.0787 Hom.: 793

Bravo AF: 0.106

Asia WGS AF: 0.0460 AC: 162 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.43
DANN	Benign	0.46
PhyloP100		-2.4

Splicing

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

Other links and lift over

dbSNP: rs906628; hg19: chr11-134738270;