rs12642469

Variant names:

• chr4-154553070-G-A
• rs12642469

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 0.187 in 152,018 control chromosomes in the GnomAD database, including 3,303 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 0.19 (3303 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.33
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.532 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: 0.187 AC: 28439 AN: 151900 Hom.: 3305 Cov.: 32

Gnomad AFR AF: 0.0919

Gnomad AMI AF: 0.312

Gnomad AMR AF: 0.212

Gnomad ASJ AF: 0.139

Gnomad EAS AF: 0.549

Gnomad SAS AF: 0.246

Gnomad FIN AF: 0.258

Gnomad MID AF: 0.150

Gnomad NFE AF: 0.198

Gnomad OTH AF: 0.184

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

GnomAD4 genome AF: 0.187 AC: 28443 AN: 152018 Hom.: 3303 Cov.: 32 AF XY: 0.193 AC XY: 14374 AN XY: 74294

African (AFR) AF: 0.0919 AC: 3812 AN: 41494

American (AMR) AF: 0.212 AC: 3236 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.139 AC: 482 AN: 3470

East Asian (EAS) AF: 0.549 AC: 2840 AN: 5172

South Asian (SAS) AF: 0.246 AC: 1182 AN: 4798

European-Finnish (FIN) AF: 0.258 AC: 2724 AN: 10560

Middle Eastern (MID) AF: 0.140 AC: 41 AN: 292

European-Non Finnish (NFE) AF: 0.198 AC: 13455 AN: 67944

Other (OTH) AF: 0.183 AC: 388 AN: 2116

Alfa AF: 0.185 Hom.: 5647

Bravo AF: 0.181

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.7
DANN	Benign	0.71
PhyloP100		1.3

Splicing

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

Other links and lift over

dbSNP: rs12642469; hg19: chr4-155474222;