ENST00000657283.1:n.2001+688G>C

Variant names:

• chr8-21110040-C-G
• rs7015657
• ENST00000518967.2:n.245+18844G>C

Variant summary

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

The ENST00000657283.1(ENSG00000254092):​n.2001+688G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.301 in 152,012 control chromosomes in the GnomAD database, including 7,126 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 0.30 (7126 hom., cov: 32)
• Consequence: ENSG00000254092 ENST00000657283.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.385
• Publications: 7 publications found

Genes affected

ENSG00000254092 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.489 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000657283.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000254092	ENST00000518967.2	TSL:2	n.245+18844G>C		intron	N/A
	ENSG00000254092	ENST00000657283.1		n.2001+688G>C		intron	N/A
	ENSG00000254092	ENST00000657734.1		n.1327-50105G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.301 AC: 45674 AN: 151892 Hom.: 7119 Cov.: 32

Gnomad AFR AF: 0.259

Gnomad AMI AF: 0.183

Gnomad AMR AF: 0.336

Gnomad ASJ AF: 0.322

Gnomad EAS AF: 0.505

Gnomad SAS AF: 0.332

Gnomad FIN AF: 0.328

Gnomad MID AF: 0.358

Gnomad NFE AF: 0.296

Gnomad OTH AF: 0.308

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

GnomAD4 genome AF: 0.301 AC: 45713 AN: 152012 Hom.: 7126 Cov.: 32 AF XY: 0.305 AC XY: 22653 AN XY: 74282

African (AFR) AF: 0.259 AC: 10742 AN: 41466

American (AMR) AF: 0.336 AC: 5133 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.322 AC: 1117 AN: 3470

East Asian (EAS) AF: 0.506 AC: 2603 AN: 5148

South Asian (SAS) AF: 0.331 AC: 1593 AN: 4810

European-Finnish (FIN) AF: 0.328 AC: 3468 AN: 10558

Middle Eastern (MID) AF: 0.354 AC: 104 AN: 294

European-Non Finnish (NFE) AF: 0.296 AC: 20130 AN: 67966

Other (OTH) AF: 0.311 AC: 656 AN: 2110

Alfa AF: 0.291 Hom.: 807

Bravo AF: 0.299

Asia WGS AF: 0.409 AC: 1423 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.8
DANN	Benign	0.59
PhyloP100		0.39

Splicing

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

Other links and lift over

dbSNP: rs7015657; hg19: chr8-20967551;