ENST00000648652.1:n.535-14263A>G

Variant names:

• chr8-92531155-T-C
• rs6989464
• ENST00000648652.1:n.535-14263A>G

Variant summary

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

The ENST00000648652.1(ENSG00000253634):​n.535-14263A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.404 in 151,522 control chromosomes in the GnomAD database, including 13,592 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 0.40 (13592 hom., cov: 32)
• Consequence: ENSG00000253634 ENST00000648652.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.60
• Publications: 1 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=-0.85).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.509 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000253634	ENST00000648652.1	n.535-14263A>G		intron_variant	Intron 4 of 13
ENSG00000253634	ENST00000744168.1	n.148-28713A>G		intron_variant	Intron 2 of 6
ENSG00000253634	ENST00000744169.1	n.151-28713A>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.404 AC: 61235 AN: 151402 Hom.: 13594 Cov.: 32

Gnomad AFR AF: 0.212

Gnomad AMI AF: 0.462

Gnomad AMR AF: 0.519

Gnomad ASJ AF: 0.516

Gnomad EAS AF: 0.341

Gnomad SAS AF: 0.500

Gnomad FIN AF: 0.479

Gnomad MID AF: 0.402

Gnomad NFE AF: 0.476

Gnomad OTH AF: 0.403

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

GnomAD4 genome AF: 0.404 AC: 61239 AN: 151522 Hom.: 13592 Cov.: 32 AF XY: 0.410 AC XY: 30327 AN XY: 74010

African (AFR) AF: 0.212 AC: 8785 AN: 41446

American (AMR) AF: 0.519 AC: 7890 AN: 15212

Ashkenazi Jewish (ASJ) AF: 0.516 AC: 1785 AN: 3460

East Asian (EAS) AF: 0.341 AC: 1757 AN: 5152

South Asian (SAS) AF: 0.499 AC: 2402 AN: 4814

European-Finnish (FIN) AF: 0.479 AC: 5031 AN: 10510

Middle Eastern (MID) AF: 0.405 AC: 119 AN: 294

European-Non Finnish (NFE) AF: 0.476 AC: 32214 AN: 67624

Other (OTH) AF: 0.398 AC: 836 AN: 2100

Alfa AF: 0.455 Hom.: 63460

Bravo AF: 0.397

Asia WGS AF: 0.420 AC: 1457 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.91
DANN	Benign	0.82
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs6989464; hg19: chr8-93543383;