2-160925262-C-T

Variant names:

• chr2-160925262-C-T
• rs1722636

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 0.288 in 151,966 control chromosomes in the GnomAD database, including 7,010 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 0.29 (7010 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.523

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.432 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: 0.287 AC: 43625 AN: 151848 Hom.: 6976 Cov.: 32

Gnomad AFR AF: 0.436

Gnomad AMI AF: 0.322

Gnomad AMR AF: 0.240

Gnomad ASJ AF: 0.273

Gnomad EAS AF: 0.185

Gnomad SAS AF: 0.287

Gnomad FIN AF: 0.217

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.227

Gnomad OTH AF: 0.278

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

GnomAD4 genome AF: 0.288 AC: 43710 AN: 151966 Hom.: 7010 Cov.: 32 AF XY: 0.284 AC XY: 21133 AN XY: 74292

Gnomad4 AFR AF: 0.437

Gnomad4 AMR AF: 0.239

Gnomad4 ASJ AF: 0.273

Gnomad4 EAS AF: 0.186

Gnomad4 SAS AF: 0.288

Gnomad4 FIN AF: 0.217

Gnomad4 NFE AF: 0.227

Gnomad4 OTH AF: 0.275

Alfa AF: 0.228 Hom.: 7523

Bravo AF: 0.294

Asia WGS AF: 0.236 AC: 821 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	9.7
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1722636; hg19: chr2-161781773;