rs12954572

Variant names:

• chr18-76111598-C-T
• rs12954572
• ENST00000848884.1:n.226+14395G>A

Variant summary

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

The ENST00000848884.1(ENSG00000310300):​n.226+14395G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.185 in 152,144 control chromosomes in the GnomAD database, including 2,644 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 (2644 hom., cov: 32)
• Consequence: ENSG00000310300 ENST00000848884.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.13
• Publications: 2 publications found

Genes affected

ENSG00000310300 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.206 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000848884.1. 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
	ENSG00000310300	ENST00000848884.1		n.226+14395G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.185 AC: 28179 AN: 152024 Hom.: 2649 Cov.: 32

Gnomad AFR AF: 0.149

Gnomad AMI AF: 0.222

Gnomad AMR AF: 0.189

Gnomad ASJ AF: 0.246

Gnomad EAS AF: 0.216

Gnomad SAS AF: 0.217

Gnomad FIN AF: 0.218

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.193

Gnomad OTH AF: 0.186

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

GnomAD4 genome AF: 0.185 AC: 28171 AN: 152144 Hom.: 2644 Cov.: 32 AF XY: 0.189 AC XY: 14059 AN XY: 74370

African (AFR) AF: 0.149 AC: 6178 AN: 41500

American (AMR) AF: 0.189 AC: 2886 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.246 AC: 853 AN: 3472

East Asian (EAS) AF: 0.216 AC: 1118 AN: 5170

South Asian (SAS) AF: 0.217 AC: 1044 AN: 4818

European-Finnish (FIN) AF: 0.218 AC: 2309 AN: 10572

Middle Eastern (MID) AF: 0.150 AC: 44 AN: 294

European-Non Finnish (NFE) AF: 0.193 AC: 13147 AN: 68002

Other (OTH) AF: 0.185 AC: 390 AN: 2110

Alfa AF: 0.190 Hom.: 2804

Bravo AF: 0.181

Asia WGS AF: 0.206 AC: 718 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.21
DANN	Benign	0.49
PhyloP100		-1.1

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: rs12954572;

hg19: chr18-73823553;

COSMIC: COSV61585548;