rs4458204

Variant names:

• chr2-227772397-C-T
• rs4458204

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 0.157 in 152,172 control chromosomes in the GnomAD database, including 2,257 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 0.16 (2257 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.73
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.249 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: 0.156 AC: 23792 AN: 152054 Hom.: 2249 Cov.: 32

Gnomad AFR AF: 0.253

Gnomad AMI AF: 0.0417

Gnomad AMR AF: 0.117

Gnomad ASJ AF: 0.132

Gnomad EAS AF: 0.0240

Gnomad SAS AF: 0.236

Gnomad FIN AF: 0.0577

Gnomad MID AF: 0.153

Gnomad NFE AF: 0.129

Gnomad OTH AF: 0.162

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

GnomAD4 genome AF: 0.157 AC: 23834 AN: 152172 Hom.: 2257 Cov.: 32 AF XY: 0.152 AC XY: 11317 AN XY: 74406

African (AFR) AF: 0.253 AC: 10497 AN: 41464

American (AMR) AF: 0.117 AC: 1786 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.132 AC: 459 AN: 3472

East Asian (EAS) AF: 0.0243 AC: 126 AN: 5190

South Asian (SAS) AF: 0.235 AC: 1135 AN: 4822

European-Finnish (FIN) AF: 0.0577 AC: 612 AN: 10604

Middle Eastern (MID) AF: 0.158 AC: 46 AN: 292

European-Non Finnish (NFE) AF: 0.129 AC: 8781 AN: 68014

Other (OTH) AF: 0.167 AC: 354 AN: 2116

Alfa AF: 0.136 Hom.: 6485

Bravo AF: 0.162

Asia WGS AF: 0.154 AC: 537 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.050
DANN	Benign	0.48
PhyloP100		-2.7

Splicing

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

Other links and lift over

dbSNP: rs4458204; hg19: chr2-228637113;