rs2155219

Variant names:

• chr11-76588150-G-T
• rs2155219

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.522 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

Gnomad4 AFR AF: 0.575

Gnomad4 AMR AF: 0.477

Gnomad4 ASJ AF: 0.634

Gnomad4 EAS AF: 0.531

Gnomad4 SAS AF: 0.506

Gnomad4 FIN AF: 0.438

Gnomad4 NFE AF: 0.505

Gnomad4 OTH AF: 0.535

Alfa AF: 0.515 Hom.: 39193

Bravo AF: 0.530

Asia WGS AF: 0.519 AC: 1805 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2155219; hg19: chr11-76299194;