2-219577768-C-T

Variant names:

• chr2-219577768-C-T
• rs2059693

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 0.309 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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.348

Gnomad4 AMR AF: 0.303

Gnomad4 ASJ AF: 0.363

Gnomad4 EAS AF: 0.245

Gnomad4 SAS AF: 0.421

Gnomad4 FIN AF: 0.242

Gnomad4 NFE AF: 0.292

Gnomad4 OTH AF: 0.332

Alfa AF: 0.296 Hom.: 13459

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2059693; hg19: chr2-220442490;