rs6472155

chr8-64817650-G-Achr8-64817650-G-Cchr8-64817650-G-T

Variant summary

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

The ENST00000665380.1(ENSG00000287998):n.367+13739G>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 0.533 in 151,880 control chromosomes in the GnomAD database, including 21,774 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 0.53 (21773 hom., cov: 31)
  • Exomes 𝑓: 0.38 (1 hom.)
• Consequence: ENST00000665380.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0400

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.689 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105375878	XR_007060941.1			upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000665380.1	n.367+13739G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.533 AC: 80823 AN: 151754 Hom.: 21743 Cov.: 31

Gnomad AFR AF: 0.544

Gnomad AMI AF: 0.337

Gnomad AMR AF: 0.565

Gnomad ASJ AF: 0.545

Gnomad EAS AF: 0.708

Gnomad SAS AF: 0.600

Gnomad FIN AF: 0.492

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.509

Gnomad OTH AF: 0.516

GnomAD4 exome AF: 0.375 AC: 3 AN: 8 Hom.: 1 AF XY: 0.375 AC XY: 3 AN XY: 8

Gnomad4 ASJ exome AF: 1.00

Gnomad4 EAS exome AF: 0.500

Gnomad4 NFE exome AF: 0.00

GnomAD4 genome AF: 0.533 AC: 80892 AN: 151872 Hom.: 21773 Cov.: 31 AF XY: 0.534 AC XY: 39604 AN XY: 74192

Gnomad4 AFR AF: 0.544

Gnomad4 AMR AF: 0.565

Gnomad4 ASJ AF: 0.545

Gnomad4 EAS AF: 0.708

Gnomad4 SAS AF: 0.601

Gnomad4 FIN AF: 0.492

Gnomad4 NFE AF: 0.510

Gnomad4 OTH AF: 0.520

Alfa AF: 0.516 Hom.: 20863

Bravo AF: 0.537

Asia WGS AF: 0.666 AC: 2312 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	3.4
Dann	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6472155; hg19: chr8-65730207;