rs13259667

chr8-77413649-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000518706.6(ENSG00000254366):n.83+14495G>A variant causes a intron, non coding transcript 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: ENST00000518706.6 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.255

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105375909	XR_001745963.2	n.84-5029G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000518706.6	n.83+14495G>A		intron_variant, non_coding_transcript_variant		3

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

Gnomad4 AFR AF: 0.0215

Gnomad4 AMR AF: 0.0549

Gnomad4 ASJ AF: 0.0372

Gnomad4 EAS AF: 0.0718

Gnomad4 SAS AF: 0.0807

Gnomad4 FIN AF: 0.0735

Gnomad4 NFE AF: 0.0736

Gnomad4 OTH AF: 0.0554

Alfa AF: 0.0700 Hom.: 192

Bravo AF: 0.0525

Asia WGS AF: 0.0670 AC: 235 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	3.5
Dann	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13259667; hg19: chr8-78325885;