rs536161

Positions:

• chr8-92500799-A-T

Variant summary

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

The ENST00000648652.1(ENSG00000253634):​n.826T>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.646 in 151,734 control chromosomes in the GnomAD database, including 32,508 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 0.65 (32507 hom., cov: 30)
  • Exomes 𝑓: 0.50 (1 hom.)
• Consequence: ENSG00000253634 ENST00000648652.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.881

Genes affected

ENSG00000253634 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.725 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105375639	XR_007061005.1	n.364T>A		non_coding_transcript_exon_variant	3/8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000253634	ENST00000648652.1	n.826T>A		non_coding_transcript_exon_variant	7/14

Frequencies

GnomAD3 genomes AF: 0.646 AC: 97909 AN: 151610 Hom.: 32501 Cov.: 30

Gnomad AFR AF: 0.498

Gnomad AMI AF: 0.789

Gnomad AMR AF: 0.574

Gnomad ASJ AF: 0.703

Gnomad EAS AF: 0.644

Gnomad SAS AF: 0.622

Gnomad FIN AF: 0.756

Gnomad MID AF: 0.709

Gnomad NFE AF: 0.731

Gnomad OTH AF: 0.659

GnomAD4 exome AF: 0.500 AC: 2 AN: 4 Hom.: 1 Cov.: 0 AF XY: 0.500 AC XY: 2 AN XY: 4

Gnomad4 NFE exome AF: 0.500

GnomAD4 genome AF: 0.646 AC: 97949 AN: 151730 Hom.: 32507 Cov.: 30 AF XY: 0.646 AC XY: 47856 AN XY: 74130

Gnomad4 AFR AF: 0.498

Gnomad4 AMR AF: 0.573

Gnomad4 ASJ AF: 0.703

Gnomad4 EAS AF: 0.644

Gnomad4 SAS AF: 0.621

Gnomad4 FIN AF: 0.756

Gnomad4 NFE AF: 0.731

Gnomad4 OTH AF: 0.658

Alfa AF: 0.679 Hom.: 4421

Bravo AF: 0.627

Asia WGS AF: 0.631 AC: 2194 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.42
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs536161; hg19: chr8-93513027;