ENST00000648652.1:n.826T>A

Variant names:

• chr8-92500799-A-T
• rs536161
• ENST00000648652.1:n.826T>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

Genes affected

ENSG00000253634 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LOC105375639	XR_007061005.1	n.364T>A		non_coding_transcript_exon_variant	Exon 3 of 8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000253634	ENST00000648652.1	n.826T>A		non_coding_transcript_exon_variant	Exon 7 of 14
ENSG00000253634	ENST00000744168.1	n.336T>A		non_coding_transcript_exon_variant	Exon 4 of 7
ENSG00000253634	ENST00000744180.1	n.364T>A		non_coding_transcript_exon_variant	Exon 3 of 5

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.500 AC: 2 AN: 4

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.498 AC: 20592 AN: 41370

American (AMR) AF: 0.573 AC: 8724 AN: 15214

Ashkenazi Jewish (ASJ) AF: 0.703 AC: 2437 AN: 3468

East Asian (EAS) AF: 0.644 AC: 3286 AN: 5100

South Asian (SAS) AF: 0.621 AC: 2988 AN: 4810

European-Finnish (FIN) AF: 0.756 AC: 7982 AN: 10560

Middle Eastern (MID) AF: 0.714 AC: 210 AN: 294

European-Non Finnish (NFE) AF: 0.731 AC: 49620 AN: 67890

Other (OTH) AF: 0.658 AC: 1392 AN: 2114

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
PhyloP100		-0.88

Splicing

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

Other links and lift over

dbSNP: rs536161; hg19: chr8-93513027;