rs13259667

Variant names:

• chr8-77413649-G-A
• rs13259667
• ENST00000518706.6:n.83+14495G>A

Variant summary

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

The ENST00000518706.6(ENSG00000254366):​n.83+14495G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0564 in 152,074 control chromosomes in the GnomAD database, including 290 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 0.056 (290 hom., cov: 32)
• Consequence: ENSG00000254366 ENST00000518706.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.255
• Publications: 2 publications found

Genes affected

ENSG00000254366 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0741 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000518706.6. 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
	ENSG00000254366	ENST00000518706.6	TSL:3	n.83+14495G>A		intron	N/A
	ENSG00000254366	ENST00000524014.2	TSL:5	n.180+14495G>A		intron	N/A
	ENSG00000254366	ENST00000733528.1		n.83+14495G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0564 AC: 8566 AN: 151956 Hom.: 290 Cov.: 32

Gnomad AFR AF: 0.0216

Gnomad AMI AF: 0.0570

Gnomad AMR AF: 0.0547

Gnomad ASJ AF: 0.0372

Gnomad EAS AF: 0.0716

Gnomad SAS AF: 0.0804

Gnomad FIN AF: 0.0735

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0736

Gnomad OTH AF: 0.0550

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

GnomAD4 genome AF: 0.0564 AC: 8572 AN: 152074 Hom.: 290 Cov.: 32 AF XY: 0.0562 AC XY: 4178 AN XY: 74344

African (AFR) AF: 0.0215 AC: 894 AN: 41556

American (AMR) AF: 0.0549 AC: 838 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.0372 AC: 129 AN: 3468

East Asian (EAS) AF: 0.0718 AC: 371 AN: 5170

South Asian (SAS) AF: 0.0807 AC: 388 AN: 4808

European-Finnish (FIN) AF: 0.0735 AC: 778 AN: 10590

Middle Eastern (MID) AF: 0.0306 AC: 9 AN: 294

European-Non Finnish (NFE) AF: 0.0736 AC: 4996 AN: 67886

Other (OTH) AF: 0.0554 AC: 117 AN: 2112

Alfa AF: 0.0700 Hom.: 218

Bravo AF: 0.0525

Asia WGS AF: 0.0670 AC: 235 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.5
DANN	Benign	0.69
PhyloP100		0.26

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: rs13259667;

hg19: chr8-78325885;