rs7398018

Variant names:

• chr12-131554797-C-T
• rs7398018
• ENST00000818348.1:n.133+3258G>A

Variant summary

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

The ENST00000818348.1(ENSG00000306424):​n.133+3258G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.388 in 152,168 control chromosomes in the GnomAD database, including 12,907 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 0.39 (12907 hom., cov: 33)
• Consequence: ENSG00000306424 ENST00000818348.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.97
• Publications: 3 publications found

Genes affected

ENSG00000306424 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.493 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000818348.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000306424	ENST00000818348.1		n.133+3258G>A		intron	N/A
	ENSG00000306424	ENST00000818349.1		n.88+5496G>A		intron	N/A
	ENSG00000306424	ENST00000818350.1		n.45+5496G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.388 AC: 58987 AN: 152050 Hom.: 12890 Cov.: 33

Gnomad AFR AF: 0.184

Gnomad AMI AF: 0.495

Gnomad AMR AF: 0.470

Gnomad ASJ AF: 0.462

Gnomad EAS AF: 0.276

Gnomad SAS AF: 0.383

Gnomad FIN AF: 0.377

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.498

Gnomad OTH AF: 0.433

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

GnomAD4 genome AF: 0.388 AC: 59031 AN: 152168 Hom.: 12907 Cov.: 33 AF XY: 0.384 AC XY: 28551 AN XY: 74378

African (AFR) AF: 0.184 AC: 7654 AN: 41514

American (AMR) AF: 0.470 AC: 7192 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.462 AC: 1603 AN: 3470

East Asian (EAS) AF: 0.275 AC: 1423 AN: 5174

South Asian (SAS) AF: 0.383 AC: 1845 AN: 4822

European-Finnish (FIN) AF: 0.377 AC: 3994 AN: 10588

Middle Eastern (MID) AF: 0.452 AC: 132 AN: 292

European-Non Finnish (NFE) AF: 0.498 AC: 33828 AN: 67994

Other (OTH) AF: 0.431 AC: 909 AN: 2110

Alfa AF: 0.420 Hom.: 2477

Bravo AF: 0.385

Asia WGS AF: 0.324 AC: 1126 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.8
DANN	Benign	0.79
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs7398018; hg19: chr12-132039342;