rs12498374

Variant names:

• chr4-110663263-C-T
• rs12498374

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 0.159 in 152,032 control chromosomes in the GnomAD database, including 2,390 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 (2390 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.830

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.29 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: 0.159 AC: 24176 AN: 151916 Hom.: 2388 Cov.: 32

Gnomad AFR AF: 0.0525

Gnomad AMI AF: 0.0844

Gnomad AMR AF: 0.142

Gnomad ASJ AF: 0.162

Gnomad EAS AF: 0.302

Gnomad SAS AF: 0.139

Gnomad FIN AF: 0.217

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.210

Gnomad OTH AF: 0.161

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

GnomAD4 genome AF: 0.159 AC: 24170 AN: 152032 Hom.: 2390 Cov.: 32 AF XY: 0.162 AC XY: 12018 AN XY: 74286

Gnomad4 AFR AF: 0.0524

Gnomad4 AMR AF: 0.142

Gnomad4 ASJ AF: 0.162

Gnomad4 EAS AF: 0.303

Gnomad4 SAS AF: 0.138

Gnomad4 FIN AF: 0.217

Gnomad4 NFE AF: 0.210

Gnomad4 OTH AF: 0.159

Alfa AF: 0.193 Hom.: 2932

Bravo AF: 0.148

Asia WGS AF: 0.196 AC: 683 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	5.3
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12498374; hg19: chr4-111584419;