2-219804017-C-T

Variant names:

• chr2-219804017-C-T
• rs3815854

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 0.509 in 152,078 control chromosomes in the GnomAD database, including 20,167 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 0.51 (20167 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.196
• Publications: 9 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.674 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: 0.509 AC: 77383 AN: 151960 Hom.: 20152 Cov.: 33

Gnomad AFR AF: 0.578

Gnomad AMI AF: 0.635

Gnomad AMR AF: 0.532

Gnomad ASJ AF: 0.580

Gnomad EAS AF: 0.692

Gnomad SAS AF: 0.476

Gnomad FIN AF: 0.475

Gnomad MID AF: 0.570

Gnomad NFE AF: 0.450

Gnomad OTH AF: 0.525

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

GnomAD4 genome AF: 0.509 AC: 77440 AN: 152078 Hom.: 20167 Cov.: 33 AF XY: 0.512 AC XY: 38078 AN XY: 74374

African (AFR) AF: 0.578 AC: 23946 AN: 41450

American (AMR) AF: 0.532 AC: 8136 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.580 AC: 2013 AN: 3468

East Asian (EAS) AF: 0.692 AC: 3584 AN: 5176

South Asian (SAS) AF: 0.474 AC: 2284 AN: 4822

European-Finnish (FIN) AF: 0.475 AC: 5023 AN: 10584

Middle Eastern (MID) AF: 0.565 AC: 166 AN: 294

European-Non Finnish (NFE) AF: 0.450 AC: 30608 AN: 67976

Other (OTH) AF: 0.522 AC: 1101 AN: 2110

Alfa AF: 0.487 Hom.: 18189

Bravo AF: 0.518

Asia WGS AF: 0.545 AC: 1893 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	6.2
DANN	Benign	0.81
PhyloP100		-0.20

Splicing

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

Other links and lift over

dbSNP: rs3815854; hg19: chr2-220668738;