rs2155219

chr11-76588150-G-T

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;