rs12373190

Variant names:

• chr18-27762081-G-A
• rs12373190
• ENST00000750368.1:n.698-15161C>T

Your query was ambiguous. Multiple possible variants found:

• chr18-27762081-G-A
• chr18-27762081-G-C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000750368.1(ENSG00000297707):​n.698-15161C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.147 in 152,084 control chromosomes in the GnomAD database, including 3,090 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 0.15 (3090 hom., cov: 32)
• Consequence: ENSG00000297707 ENST00000750368.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.751
• Publications: 2 publications found

Genes affected

ENSG00000297707 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.365 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
ENSG00000297707	ENST00000750368.1	n.698-15161C>T		intron_variant	Intron 3 of 4
ENSG00000297707	ENST00000750369.1	n.302-15161C>T		intron_variant	Intron 2 of 4
ENSG00000297707	ENST00000750370.1	n.244-15161C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.147 AC: 22282 AN: 151966 Hom.: 3074 Cov.: 32

Gnomad AFR AF: 0.369

Gnomad AMI AF: 0.0779

Gnomad AMR AF: 0.0732

Gnomad ASJ AF: 0.0536

Gnomad EAS AF: 0.103

Gnomad SAS AF: 0.0270

Gnomad FIN AF: 0.0474

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0621

Gnomad OTH AF: 0.121

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

GnomAD4 genome AF: 0.147 AC: 22337 AN: 152084 Hom.: 3090 Cov.: 32 AF XY: 0.143 AC XY: 10604 AN XY: 74340

African (AFR) AF: 0.369 AC: 15311 AN: 41448

American (AMR) AF: 0.0731 AC: 1115 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.0536 AC: 186 AN: 3470

East Asian (EAS) AF: 0.103 AC: 534 AN: 5176

South Asian (SAS) AF: 0.0272 AC: 131 AN: 4818

European-Finnish (FIN) AF: 0.0474 AC: 503 AN: 10602

Middle Eastern (MID) AF: 0.0306 AC: 9 AN: 294

European-Non Finnish (NFE) AF: 0.0621 AC: 4225 AN: 67994

Other (OTH) AF: 0.119 AC: 252 AN: 2110

Alfa AF: 0.0749 Hom.: 972

Bravo AF: 0.161

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.33
DANN	Benign	0.63
PhyloP100		-0.75

Splicing

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

Other links and lift over

dbSNP: rs12373190; hg19: chr18-25342045;