rs4499362

Variant names:

• chr2-148810827-C-T
• rs4499362

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 0.253 in 152,072 control chromosomes in the GnomAD database, including 5,189 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 (5189 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.75
• Publications: 18 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.39 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: 0.253 AC: 38413 AN: 151956 Hom.: 5167 Cov.: 32

Gnomad AFR AF: 0.304

Gnomad AMI AF: 0.312

Gnomad AMR AF: 0.291

Gnomad ASJ AF: 0.218

Gnomad EAS AF: 0.352

Gnomad SAS AF: 0.404

Gnomad FIN AF: 0.238

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.198

Gnomad OTH AF: 0.251

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

GnomAD4 genome AF: 0.253 AC: 38493 AN: 152072 Hom.: 5189 Cov.: 32 AF XY: 0.258 AC XY: 19177 AN XY: 74328

African (AFR) AF: 0.305 AC: 12637 AN: 41486

American (AMR) AF: 0.291 AC: 4453 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.218 AC: 758 AN: 3472

East Asian (EAS) AF: 0.353 AC: 1817 AN: 5152

South Asian (SAS) AF: 0.405 AC: 1945 AN: 4808

European-Finnish (FIN) AF: 0.238 AC: 2517 AN: 10572

Middle Eastern (MID) AF: 0.177 AC: 52 AN: 294

European-Non Finnish (NFE) AF: 0.198 AC: 13487 AN: 67986

Other (OTH) AF: 0.257 AC: 543 AN: 2112

Alfa AF: 0.225 Hom.: 13441

Bravo AF: 0.262

Asia WGS AF: 0.408 AC: 1419 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.16
DANN	Benign	0.40
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs4499362; hg19: chr2-149568396;