rs4667492

Variant names:

• chr2-165731192-T-C
• rs4667492

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 0.26 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
• Publications: 7 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.196 AC: 8112 AN: 41476

American (AMR) AF: 0.263 AC: 4008 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.283 AC: 981 AN: 3468

East Asian (EAS) AF: 0.385 AC: 1990 AN: 5164

South Asian (SAS) AF: 0.430 AC: 2073 AN: 4824

European-Finnish (FIN) AF: 0.273 AC: 2870 AN: 10532

Middle Eastern (MID) AF: 0.276 AC: 81 AN: 294

European-Non Finnish (NFE) AF: 0.273 AC: 18565 AN: 67946

Other (OTH) AF: 0.267 AC: 561 AN: 2102

Alfa AF: 0.277 Hom.: 11579

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
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs4667492; hg19: chr2-166587702;