rs4667492

Positions:

• chr2-165731192-T-C

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 0.26 in 151,984 control chromosomes in the GnomAD database, including 5,367 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 0.26 (5367 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.214

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.59).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.414 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.260 AC: 39462 AN: 151866 Hom.: 5369 Cov.: 32

Gnomad AFR AF: 0.196

Gnomad AMI AF: 0.254

Gnomad AMR AF: 0.262

Gnomad ASJ AF: 0.283

Gnomad EAS AF: 0.386

Gnomad SAS AF: 0.430

Gnomad FIN AF: 0.273

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.273

Gnomad OTH AF: 0.269

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

GnomAD4 genome AF: 0.260 AC: 39473 AN: 151984 Hom.: 5367 Cov.: 32 AF XY: 0.262 AC XY: 19473 AN XY: 74276

Gnomad4 AFR AF: 0.196

Gnomad4 AMR AF: 0.263

Gnomad4 ASJ AF: 0.283

Gnomad4 EAS AF: 0.385

Gnomad4 SAS AF: 0.430

Gnomad4 FIN AF: 0.273

Gnomad4 NFE AF: 0.273

Gnomad4 OTH AF: 0.267

Alfa AF: 0.282 Hom.: 3511

Bravo AF: 0.256

Asia WGS AF: 0.372 AC: 1285 AN: 3458

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.59
CADD	Benign	8.7
DANN	Benign	0.97

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4667492; hg19: chr2-166587702;