2-191165665-C-T

Variant names:

• chr2-191165665-C-T
• rs1869624

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 0.252 in 152,100 control chromosomes in the GnomAD database, including 5,214 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 0.25 (5214 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.132

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.3 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: 0.252 AC: 38271 AN: 151982 Hom.: 5216 Cov.: 32

Gnomad AFR AF: 0.195

Gnomad AMI AF: 0.107

Gnomad AMR AF: 0.227

Gnomad ASJ AF: 0.336

Gnomad EAS AF: 0.181

Gnomad SAS AF: 0.176

Gnomad FIN AF: 0.224

Gnomad MID AF: 0.405

Gnomad NFE AF: 0.303

Gnomad OTH AF: 0.284

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

GnomAD4 genome AF: 0.252 AC: 38274 AN: 152100 Hom.: 5214 Cov.: 32 AF XY: 0.244 AC XY: 18147 AN XY: 74346

Gnomad4 AFR AF: 0.195

Gnomad4 AMR AF: 0.227

Gnomad4 ASJ AF: 0.336

Gnomad4 EAS AF: 0.180

Gnomad4 SAS AF: 0.177

Gnomad4 FIN AF: 0.224

Gnomad4 NFE AF: 0.303

Gnomad4 OTH AF: 0.282

Alfa AF: 0.282 Hom.: 4845

Bravo AF: 0.249

Asia WGS AF: 0.164 AC: 573 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.5
DANN	Benign	0.16

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1869624; hg19: chr2-192030391;