2-219577768-C-T

Variant names:

• chr2-219577768-C-T
• rs2059693

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 0.309 in 151,840 control chromosomes in the GnomAD database, including 7,478 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 0.31 (7478 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.77
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.406 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: 0.309 AC: 46898 AN: 151722 Hom.: 7477 Cov.: 31

Gnomad AFR AF: 0.349

Gnomad AMI AF: 0.137

Gnomad AMR AF: 0.303

Gnomad ASJ AF: 0.363

Gnomad EAS AF: 0.245

Gnomad SAS AF: 0.422

Gnomad FIN AF: 0.242

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.292

Gnomad OTH AF: 0.335

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

GnomAD4 genome AF: 0.309 AC: 46919 AN: 151840 Hom.: 7478 Cov.: 31 AF XY: 0.308 AC XY: 22859 AN XY: 74186

African (AFR) AF: 0.348 AC: 14423 AN: 41402

American (AMR) AF: 0.303 AC: 4619 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.363 AC: 1260 AN: 3472

East Asian (EAS) AF: 0.245 AC: 1261 AN: 5152

South Asian (SAS) AF: 0.421 AC: 2026 AN: 4810

European-Finnish (FIN) AF: 0.242 AC: 2542 AN: 10488

Middle Eastern (MID) AF: 0.384 AC: 113 AN: 294

European-Non Finnish (NFE) AF: 0.292 AC: 19852 AN: 67952

Other (OTH) AF: 0.332 AC: 699 AN: 2108

Alfa AF: 0.299 Hom.: 28421

Bravo AF: 0.314

Asia WGS AF: 0.311 AC: 1077 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	2.1
DANN	Benign	0.79
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs2059693; hg19: chr2-220442490;