chr2-191166501-G-T

Variant names:

• chr2-191166501-G-T
• rs4853550

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 0.681 in 152,128 control chromosomes in the GnomAD database, including 37,431 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 0.68 (37431 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0340

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.79 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: 0.681 AC: 103552 AN: 152010 Hom.: 37419 Cov.: 33

Gnomad AFR AF: 0.440

Gnomad AMI AF: 0.865

Gnomad AMR AF: 0.775

Gnomad ASJ AF: 0.858

Gnomad EAS AF: 0.443

Gnomad SAS AF: 0.775

Gnomad FIN AF: 0.743

Gnomad MID AF: 0.722

Gnomad NFE AF: 0.796

Gnomad OTH AF: 0.720

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

GnomAD4 genome AF: 0.681 AC: 103610 AN: 152128 Hom.: 37431 Cov.: 33 AF XY: 0.682 AC XY: 50714 AN XY: 74364

Gnomad4 AFR AF: 0.440

Gnomad4 AMR AF: 0.775

Gnomad4 ASJ AF: 0.858

Gnomad4 EAS AF: 0.444

Gnomad4 SAS AF: 0.774

Gnomad4 FIN AF: 0.743

Gnomad4 NFE AF: 0.796

Gnomad4 OTH AF: 0.720

Alfa AF: 0.776 Hom.: 45418

Bravo AF: 0.672

Asia WGS AF: 0.609 AC: 2120 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	7.4
DANN	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4853550; hg19: chr2-192031227;