2-219807447-C-T

Variant names:

• chr2-219807447-C-T
• rs2113855

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 0.948 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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.977 AC: 40603 AN: 41556

American (AMR) AF: 0.962 AC: 14708 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.959 AC: 3330 AN: 3472

East Asian (EAS) AF: 1.00 AC: 5190 AN: 5192

South Asian (SAS) AF: 0.949 AC: 4577 AN: 4822

European-Finnish (FIN) AF: 0.937 AC: 9893 AN: 10562

Middle Eastern (MID) AF: 0.946 AC: 278 AN: 294

European-Non Finnish (NFE) AF: 0.923 AC: 62764 AN: 67974

Other (OTH) AF: 0.946 AC: 1999 AN: 2112

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
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs2113855; hg19: chr2-220672168;