rs12373417

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 6 publications found

Genes affected

ENSG00000266049 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000581172.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000266049	ENST00000581172.1	TSL:3	n.450+2174C>T		intron	N/A
	ENSG00000266049	ENST00000583546.1	TSL:3	n.308+2174C>T		intron	N/A

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

African (AFR) AF: 0.0506 AC: 2096 AN: 41404

American (AMR) AF: 0.259 AC: 3959 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.219 AC: 759 AN: 3468

East Asian (EAS) AF: 0.162 AC: 837 AN: 5172

South Asian (SAS) AF: 0.168 AC: 811 AN: 4824

European-Finnish (FIN) AF: 0.295 AC: 3118 AN: 10558

Middle Eastern (MID) AF: 0.153 AC: 45 AN: 294

European-Non Finnish (NFE) AF: 0.246 AC: 16692 AN: 67984

Other (OTH) AF: 0.195 AC: 412 AN: 2114

Alfa AF: 0.231 Hom.: 3696

Bravo AF: 0.184

Asia WGS AF: 0.160 AC: 553 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	12
DANN	Benign	0.60
PhyloP100		0.34

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs12373417;

hg19: chr18-2830440;