11-134612572-T-C

Variant names:

• chr11-134612572-T-C
• rs1944866

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 0.2 in 152,114 control chromosomes in the GnomAD database, including 3,884 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 0.20 (3884 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.914
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.354 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: 0.200 AC: 30354 AN: 151996 Hom.: 3874 Cov.: 32

Gnomad AFR AF: 0.359

Gnomad AMI AF: 0.189

Gnomad AMR AF: 0.149

Gnomad ASJ AF: 0.192

Gnomad EAS AF: 0.319

Gnomad SAS AF: 0.167

Gnomad FIN AF: 0.0884

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.126

Gnomad OTH AF: 0.190

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

GnomAD4 genome AF: 0.200 AC: 30403 AN: 152114 Hom.: 3884 Cov.: 32 AF XY: 0.198 AC XY: 14765 AN XY: 74390

African (AFR) AF: 0.359 AC: 14891 AN: 41458

American (AMR) AF: 0.149 AC: 2274 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.192 AC: 665 AN: 3466

East Asian (EAS) AF: 0.319 AC: 1646 AN: 5160

South Asian (SAS) AF: 0.166 AC: 801 AN: 4814

European-Finnish (FIN) AF: 0.0884 AC: 938 AN: 10610

Middle Eastern (MID) AF: 0.126 AC: 37 AN: 294

European-Non Finnish (NFE) AF: 0.126 AC: 8581 AN: 67994

Other (OTH) AF: 0.189 AC: 398 AN: 2110

Alfa AF: 0.156 Hom.: 4333

Bravo AF: 0.212

Asia WGS AF: 0.236 AC: 820 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.5
DANN	Benign	0.79
PhyloP100		0.91

Splicing

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

Other links and lift over

dbSNP: rs1944866; hg19: chr11-134482466;