rs12373417

Variant names:

• chr18-2830442-G-A
• rs12373417
• ENST00000581172.1:n.450+2174C>T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000581172.1(ENSG00000266049):​n.450+2174C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.191 in 152,006 control chromosomes in the GnomAD database, including 3,472 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 (3472 hom., cov: 32)
• Consequence: ENSG00000266049 ENST00000581172.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.343

Genes affected

ENSG00000266049 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.252 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
ENSG00000266049	ENST00000581172.1	n.450+2174C>T		intron_variant	Intron 1 of 1	3
ENSG00000266049	ENST00000583546.1	n.308+2174C>T		intron_variant	Intron 1 of 3	3

Frequencies

GnomAD3 genomes AF: 0.191 AC: 28975 AN: 151888 Hom.: 3467 Cov.: 32

Gnomad AFR AF: 0.0508

Gnomad AMI AF: 0.286

Gnomad AMR AF: 0.259

Gnomad ASJ AF: 0.219

Gnomad EAS AF: 0.162

Gnomad SAS AF: 0.166

Gnomad FIN AF: 0.295

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.245

Gnomad OTH AF: 0.196

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

GnomAD4 genome AF: 0.191 AC: 28990 AN: 152006 Hom.: 3472 Cov.: 32 AF XY: 0.193 AC XY: 14374 AN XY: 74292

Gnomad4 AFR AF: 0.0506

Gnomad4 AMR AF: 0.259

Gnomad4 ASJ AF: 0.219

Gnomad4 EAS AF: 0.162

Gnomad4 SAS AF: 0.168

Gnomad4 FIN AF: 0.295

Gnomad4 NFE AF: 0.246

Gnomad4 OTH AF: 0.195

Alfa AF: 0.232 Hom.: 3169

Bravo AF: 0.184

Asia WGS AF: 0.160 AC: 553 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	12
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12373417; hg19: chr18-2830440;