rs12953809

Variant names:

• chr18-77246693-C-T
• rs12953809
• ENST00000844037.1:n.162+4155G>A

Variant summary

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

The ENST00000844037.1(ENSG00000309801):​n.162+4155G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0619 in 152,198 control chromosomes in the GnomAD database, including 352 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 0.062 (352 hom., cov: 32)
• Consequence: ENSG00000309801 ENST00000844037.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.28
• Publications: 0 publications found

Genes affected

ENSG00000309801 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.09).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0848 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000844037.1. 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
	ENSG00000309801	ENST00000844037.1		n.162+4155G>A		intron	N/A
	ENSG00000309801	ENST00000844038.1		n.118+4108G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0618 AC: 9399 AN: 152080 Hom.: 347 Cov.: 32

Gnomad AFR AF: 0.0208

Gnomad AMI AF: 0.0384

Gnomad AMR AF: 0.0547

Gnomad ASJ AF: 0.0467

Gnomad EAS AF: 0.0359

Gnomad SAS AF: 0.0731

Gnomad FIN AF: 0.0837

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.0866

Gnomad OTH AF: 0.0728

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

GnomAD4 genome AF: 0.0619 AC: 9418 AN: 152198 Hom.: 352 Cov.: 32 AF XY: 0.0611 AC XY: 4547 AN XY: 74400

African (AFR) AF: 0.0207 AC: 860 AN: 41526

American (AMR) AF: 0.0546 AC: 835 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0467 AC: 162 AN: 3470

East Asian (EAS) AF: 0.0358 AC: 185 AN: 5168

South Asian (SAS) AF: 0.0742 AC: 358 AN: 4824

European-Finnish (FIN) AF: 0.0837 AC: 886 AN: 10582

Middle Eastern (MID) AF: 0.126 AC: 37 AN: 294

European-Non Finnish (NFE) AF: 0.0866 AC: 5891 AN: 68018

Other (OTH) AF: 0.0801 AC: 169 AN: 2110

Alfa AF: 0.0758 Hom.: 350

Bravo AF: 0.0584

Asia WGS AF: 0.0790 AC: 272 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.28
DANN	Benign	0.74
PhyloP100		-2.3

Splicing

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

Other links and lift over

dbSNP: rs12953809; hg19: chr18-74958649;