rs2155219

Variant names:

• chr11-76588150-G-T
• rs2155219

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 0.522 in 151,938 control chromosomes in the GnomAD database, including 20,888 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 0.52 (20888 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.619
• Publications: 104 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.569 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.522 AC: 79264 AN: 151820 Hom.: 20882 Cov.: 33

Gnomad AFR AF: 0.575

Gnomad AMI AF: 0.704

Gnomad AMR AF: 0.478

Gnomad ASJ AF: 0.634

Gnomad EAS AF: 0.532

Gnomad SAS AF: 0.506

Gnomad FIN AF: 0.438

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.505

Gnomad OTH AF: 0.539

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

GnomAD4 genome AF: 0.522 AC: 79307 AN: 151938 Hom.: 20888 Cov.: 33 AF XY: 0.518 AC XY: 38480 AN XY: 74242

African (AFR) AF: 0.575 AC: 23830 AN: 41432

American (AMR) AF: 0.477 AC: 7290 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.634 AC: 2198 AN: 3468

East Asian (EAS) AF: 0.531 AC: 2741 AN: 5158

South Asian (SAS) AF: 0.506 AC: 2440 AN: 4820

European-Finnish (FIN) AF: 0.438 AC: 4621 AN: 10546

Middle Eastern (MID) AF: 0.476 AC: 139 AN: 292

European-Non Finnish (NFE) AF: 0.505 AC: 34279 AN: 67930

Other (OTH) AF: 0.535 AC: 1128 AN: 2108

Alfa AF: 0.513 Hom.: 83134

Bravo AF: 0.530

Asia WGS AF: 0.519 AC: 1805 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.57
DANN	Benign	0.64
PhyloP100		-0.62

Splicing

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

Other links and lift over

dbSNP: rs2155219; hg19: chr11-76299194;