11-55810222-T-C

Variant names:

• chr11-55810222-T-C
• rs984371

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 0.178 in 152,016 control chromosomes in the GnomAD database, including 2,611 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 0.18 (2611 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0200
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.21 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: 0.178 AC: 27051 AN: 151898 Hom.: 2614 Cov.: 32

Gnomad AFR AF: 0.103

Gnomad AMI AF: 0.261

Gnomad AMR AF: 0.216

Gnomad ASJ AF: 0.283

Gnomad EAS AF: 0.152

Gnomad SAS AF: 0.193

Gnomad FIN AF: 0.177

Gnomad MID AF: 0.159

Gnomad NFE AF: 0.210

Gnomad OTH AF: 0.164

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

GnomAD4 genome AF: 0.178 AC: 27048 AN: 152016 Hom.: 2611 Cov.: 32 AF XY: 0.178 AC XY: 13216 AN XY: 74302

African (AFR) AF: 0.103 AC: 4252 AN: 41420

American (AMR) AF: 0.216 AC: 3295 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.283 AC: 983 AN: 3468

East Asian (EAS) AF: 0.152 AC: 785 AN: 5164

South Asian (SAS) AF: 0.194 AC: 934 AN: 4818

European-Finnish (FIN) AF: 0.177 AC: 1876 AN: 10592

Middle Eastern (MID) AF: 0.147 AC: 43 AN: 292

European-Non Finnish (NFE) AF: 0.210 AC: 14299 AN: 67970

Other (OTH) AF: 0.163 AC: 343 AN: 2108

Alfa AF: 0.203 Hom.: 5944

Bravo AF: 0.176

Asia WGS AF: 0.152 AC: 531 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	4.1
DANN	Benign	0.56
PhyloP100		-0.020

Splicing

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

Other links and lift over

dbSNP: rs984371; hg19: chr11-55577698;