rs12189790

Variant names:

• chr6-18060076-G-A
• rs12189790
• ENST00000747204.1:n.156+4324G>A

Variant summary

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

The ENST00000747204.1(ENSG00000297344):​n.156+4324G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.179 in 151,604 control chromosomes in the GnomAD database, including 2,729 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 0.18 (2729 hom., cov: 33)
• Consequence: ENSG00000297344 ENST00000747204.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.850
• Publications: 2 publications found

Genes affected

ENSG00000297344 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.269 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
ENSG00000297344	ENST00000747204.1	n.156+4324G>A		intron_variant	Intron 2 of 3
ENSG00000297344	ENST00000747205.1	n.246+4324G>A		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.179 AC: 27149 AN: 151486 Hom.: 2720 Cov.: 33

Gnomad AFR AF: 0.272

Gnomad AMI AF: 0.132

Gnomad AMR AF: 0.130

Gnomad ASJ AF: 0.197

Gnomad EAS AF: 0.00250

Gnomad SAS AF: 0.157

Gnomad FIN AF: 0.119

Gnomad MID AF: 0.240

Gnomad NFE AF: 0.158

Gnomad OTH AF: 0.172

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

GnomAD4 genome AF: 0.179 AC: 27186 AN: 151604 Hom.: 2729 Cov.: 33 AF XY: 0.176 AC XY: 13058 AN XY: 74150

African (AFR) AF: 0.273 AC: 11294 AN: 41406

American (AMR) AF: 0.130 AC: 1985 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.197 AC: 684 AN: 3472

East Asian (EAS) AF: 0.00251 AC: 13 AN: 5186

South Asian (SAS) AF: 0.156 AC: 751 AN: 4810

European-Finnish (FIN) AF: 0.119 AC: 1258 AN: 10536

Middle Eastern (MID) AF: 0.234 AC: 67 AN: 286

European-Non Finnish (NFE) AF: 0.157 AC: 10653 AN: 67644

Other (OTH) AF: 0.171 AC: 361 AN: 2106

Alfa AF: 0.166 Hom.: 930

Bravo AF: 0.181

Asia WGS AF: 0.0880 AC: 306 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.56
DANN	Benign	0.29
PhyloP100		-0.85

Splicing

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

Other links and lift over

dbSNP: rs12189790; hg19: chr6-18060307;