chr11-55362164-C-T

Variant names:

• chr11-55362164-C-T
• rs11229252

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 0.088 in 151,768 control chromosomes in the GnomAD database, including 812 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 0.088 (812 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.24
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.129 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: 0.0882 AC: 13373 AN: 151650 Hom.: 812 Cov.: 32

Gnomad AFR AF: 0.0218

Gnomad AMI AF: 0.0362

Gnomad AMR AF: 0.0905

Gnomad ASJ AF: 0.0580

Gnomad EAS AF: 0.137

Gnomad SAS AF: 0.107

Gnomad FIN AF: 0.204

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.108

Gnomad OTH AF: 0.0730

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

GnomAD4 genome AF: 0.0880 AC: 13361 AN: 151768 Hom.: 812 Cov.: 32 AF XY: 0.0929 AC XY: 6886 AN XY: 74112

African (AFR) AF: 0.0217 AC: 901 AN: 41466

American (AMR) AF: 0.0903 AC: 1372 AN: 15202

Ashkenazi Jewish (ASJ) AF: 0.0580 AC: 201 AN: 3464

East Asian (EAS) AF: 0.137 AC: 701 AN: 5118

South Asian (SAS) AF: 0.107 AC: 516 AN: 4818

European-Finnish (FIN) AF: 0.204 AC: 2150 AN: 10538

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.108 AC: 7309 AN: 67852

Other (OTH) AF: 0.0713 AC: 150 AN: 2104

Alfa AF: 0.0963 Hom.: 114

Bravo AF: 0.0768

Asia WGS AF: 0.0840 AC: 292 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.015
DANN	Benign	0.20
PhyloP100		-3.2

Splicing

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

Other links and lift over

dbSNP: rs11229252; hg19: chr11-55129640; COSMIC: COSV107158459;