rs2155225

Variant names:

• chr11-76640853-A-T
• rs2155225

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 0.603 in 151,850 control chromosomes in the GnomAD database, including 29,009 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 0.60 (29009 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.960
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.801 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.603 AC: 91490 AN: 151732 Hom.: 28963 Cov.: 33

Gnomad AFR AF: 0.808

Gnomad AMI AF: 0.620

Gnomad AMR AF: 0.447

Gnomad ASJ AF: 0.526

Gnomad EAS AF: 0.603

Gnomad SAS AF: 0.577

Gnomad FIN AF: 0.540

Gnomad MID AF: 0.604

Gnomad NFE AF: 0.530

Gnomad OTH AF: 0.573

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

GnomAD4 genome AF: 0.603 AC: 91589 AN: 151850 Hom.: 29009 Cov.: 33 AF XY: 0.601 AC XY: 44618 AN XY: 74206

African (AFR) AF: 0.808 AC: 33491 AN: 41430

American (AMR) AF: 0.446 AC: 6817 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.526 AC: 1822 AN: 3466

East Asian (EAS) AF: 0.604 AC: 3092 AN: 5122

South Asian (SAS) AF: 0.577 AC: 2782 AN: 4820

European-Finnish (FIN) AF: 0.540 AC: 5687 AN: 10536

Middle Eastern (MID) AF: 0.599 AC: 176 AN: 294

European-Non Finnish (NFE) AF: 0.530 AC: 35945 AN: 67874

Other (OTH) AF: 0.574 AC: 1212 AN: 2112

Alfa AF: 0.576 Hom.: 3207

Bravo AF: 0.604

Asia WGS AF: 0.632 AC: 2199 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	1.8
DANN	Benign	0.75
PhyloP100		-0.96

Splicing

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

Other links and lift over

dbSNP: rs2155225; hg19: chr11-76351897; COSMIC: COSV101249377;