ENST00000648652.1:n.1195+1388A>C

Variant names:

• chr8-92470335-T-G
• rs2046129
• ENST00000648652.1:n.1195+1388A>C

Variant summary

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

The ENST00000648652.1(ENSG00000253634):​n.1195+1388A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.354 in 152,160 control chromosomes in the GnomAD database, including 9,719 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 0.35 (9719 hom., cov: 33)
• Consequence: ENSG00000253634 ENST00000648652.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.127
• 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=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.436 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000648652.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000253634	ENST00000648652.1		n.1195+1388A>C		intron	N/A
	ENSG00000253634	ENST00000744168.1		n.540+1388A>C		intron	N/A
	ENSG00000253634	ENST00000744176.1		n.100-4684A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.354 AC: 53834 AN: 152042 Hom.: 9715 Cov.: 33

Gnomad AFR AF: 0.441

Gnomad AMI AF: 0.537

Gnomad AMR AF: 0.312

Gnomad ASJ AF: 0.389

Gnomad EAS AF: 0.221

Gnomad SAS AF: 0.241

Gnomad FIN AF: 0.328

Gnomad MID AF: 0.320

Gnomad NFE AF: 0.330

Gnomad OTH AF: 0.326

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

GnomAD4 genome AF: 0.354 AC: 53876 AN: 152160 Hom.: 9719 Cov.: 33 AF XY: 0.350 AC XY: 26062 AN XY: 74396

African (AFR) AF: 0.441 AC: 18302 AN: 41498

American (AMR) AF: 0.311 AC: 4758 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.389 AC: 1349 AN: 3472

East Asian (EAS) AF: 0.221 AC: 1142 AN: 5176

South Asian (SAS) AF: 0.241 AC: 1165 AN: 4826

European-Finnish (FIN) AF: 0.328 AC: 3471 AN: 10576

Middle Eastern (MID) AF: 0.330 AC: 97 AN: 294

European-Non Finnish (NFE) AF: 0.330 AC: 22420 AN: 68010

Other (OTH) AF: 0.323 AC: 682 AN: 2112

Alfa AF: 0.244 Hom.: 813

Bravo AF: 0.359

Asia WGS AF: 0.225 AC: 783 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.37
DANN	Benign	0.57
PhyloP100		-0.13

Splicing

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

Other links and lift over

dbSNP: rs2046129; hg19: chr8-93482563;