2-219807447-C-T

Variant names:

• chr2-219807447-C-T
• rs2113855

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 0.948 in 152,178 control chromosomes in the GnomAD database, including 68,412 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 0.95 (68412 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.02

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 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: 0.948 AC: 144113 AN: 152060 Hom.: 68353 Cov.: 32

Gnomad AFR AF: 0.977

Gnomad AMI AF: 0.975

Gnomad AMR AF: 0.962

Gnomad ASJ AF: 0.959

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.949

Gnomad FIN AF: 0.937

Gnomad MID AF: 0.949

Gnomad NFE AF: 0.923

Gnomad OTH AF: 0.946

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

GnomAD4 genome AF: 0.948 AC: 144231 AN: 152178 Hom.: 68412 Cov.: 32 AF XY: 0.950 AC XY: 70687 AN XY: 74410

Gnomad4 AFR AF: 0.977

Gnomad4 AMR AF: 0.962

Gnomad4 ASJ AF: 0.959

Gnomad4 EAS AF: 1.00

Gnomad4 SAS AF: 0.949

Gnomad4 FIN AF: 0.937

Gnomad4 NFE AF: 0.923

Gnomad4 OTH AF: 0.946

Alfa AF: 0.928 Hom.: 8138

Bravo AF: 0.952

Asia WGS AF: 0.981 AC: 3405 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.91
DANN	Benign	0.29

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2113855; hg19: chr2-220672168;