11-134578921-A-C

Variant names:

• chr11-134578921-A-C
• rs10894846

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 0.25 in 152,046 control chromosomes in the GnomAD database, including 5,518 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 0.25 (5518 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.02
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.515 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: 0.250 AC: 38045 AN: 151928 Hom.: 5500 Cov.: 33

Gnomad AFR AF: 0.332

Gnomad AMI AF: 0.103

Gnomad AMR AF: 0.342

Gnomad ASJ AF: 0.224

Gnomad EAS AF: 0.531

Gnomad SAS AF: 0.184

Gnomad FIN AF: 0.142

Gnomad MID AF: 0.332

Gnomad NFE AF: 0.184

Gnomad OTH AF: 0.250

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

GnomAD4 genome AF: 0.250 AC: 38087 AN: 152046 Hom.: 5518 Cov.: 33 AF XY: 0.252 AC XY: 18749 AN XY: 74326

African (AFR) AF: 0.332 AC: 13752 AN: 41442

American (AMR) AF: 0.343 AC: 5239 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.224 AC: 775 AN: 3464

East Asian (EAS) AF: 0.531 AC: 2723 AN: 5126

South Asian (SAS) AF: 0.184 AC: 886 AN: 4828

European-Finnish (FIN) AF: 0.142 AC: 1505 AN: 10600

Middle Eastern (MID) AF: 0.333 AC: 98 AN: 294

European-Non Finnish (NFE) AF: 0.184 AC: 12495 AN: 67990

Other (OTH) AF: 0.247 AC: 520 AN: 2108

Alfa AF: 0.223 Hom.: 1746

Bravo AF: 0.277

Asia WGS AF: 0.323 AC: 1120 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.036
DANN	Benign	0.23
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs10894846; hg19: chr11-134448815;