rs12518194

Variant names:

• chr5-25951452-A-G
• rs12518194
• ENST00000805125.1:n.188+384A>G

Variant summary

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

The ENST00000805125.1(ENSG00000304648):​n.188+384A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.275 in 151,748 control chromosomes in the GnomAD database, including 7,310 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 0.28 (7310 hom., cov: 32)
• Consequence: ENSG00000304648 ENST00000805125.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0700
• Publications: 9 publications found

Genes affected

ENSG00000304648 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.372 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
ENSG00000304648	ENST00000805125.1	n.188+384A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.275 AC: 41761 AN: 151630 Hom.: 7309 Cov.: 32

Gnomad AFR AF: 0.0698

Gnomad AMI AF: 0.355

Gnomad AMR AF: 0.268

Gnomad ASJ AF: 0.457

Gnomad EAS AF: 0.152

Gnomad SAS AF: 0.309

Gnomad FIN AF: 0.417

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.376

Gnomad OTH AF: 0.300

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

GnomAD4 genome AF: 0.275 AC: 41767 AN: 151748 Hom.: 7310 Cov.: 32 AF XY: 0.278 AC XY: 20575 AN XY: 74138

African (AFR) AF: 0.0697 AC: 2893 AN: 41496

American (AMR) AF: 0.267 AC: 4062 AN: 15196

Ashkenazi Jewish (ASJ) AF: 0.457 AC: 1583 AN: 3466

East Asian (EAS) AF: 0.153 AC: 780 AN: 5104

South Asian (SAS) AF: 0.311 AC: 1498 AN: 4818

European-Finnish (FIN) AF: 0.417 AC: 4400 AN: 10558

Middle Eastern (MID) AF: 0.425 AC: 125 AN: 294

European-Non Finnish (NFE) AF: 0.376 AC: 25470 AN: 67800

Other (OTH) AF: 0.301 AC: 633 AN: 2106

Alfa AF: 0.339 Hom.: 5197

Bravo AF: 0.256

Asia WGS AF: 0.240 AC: 834 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.3
DANN	Benign	0.47
PhyloP100		0.070

Splicing

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

Other links and lift over

dbSNP: rs12518194; hg19: chr5-25951561; COSMIC: COSV54957365;