ENST00000657734.1:n.1326+23586C>T

Variant names:

• chr8-21271548-G-A
• rs2631878
• ENST00000657734.1:n.1326+23586C>T

Variant summary

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

The ENST00000657734.1(ENSG00000254092):​n.1326+23586C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.246 in 152,054 control chromosomes in the GnomAD database, including 8,032 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 0.25 (8032 hom., cov: 32)
• Consequence: ENSG00000254092 ENST00000657734.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.238
• Publications: 1 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 (AFR) allele frequency at 95% confidence interval = 0.577 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000657734.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000254092	ENST00000657734.1		n.1326+23586C>T		intron	N/A
	ENSG00000254092	ENST00000659453.1		n.1639+23586C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.246 AC: 37354 AN: 151936 Hom.: 8014 Cov.: 32

Gnomad AFR AF: 0.583

Gnomad AMI AF: 0.0877

Gnomad AMR AF: 0.170

Gnomad ASJ AF: 0.146

Gnomad EAS AF: 0.0250

Gnomad SAS AF: 0.117

Gnomad FIN AF: 0.0734

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.119

Gnomad OTH AF: 0.233

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

GnomAD4 genome AF: 0.246 AC: 37408 AN: 152054 Hom.: 8032 Cov.: 32 AF XY: 0.239 AC XY: 17750 AN XY: 74362

African (AFR) AF: 0.583 AC: 24144 AN: 41422

American (AMR) AF: 0.169 AC: 2588 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.146 AC: 508 AN: 3472

East Asian (EAS) AF: 0.0250 AC: 129 AN: 5152

South Asian (SAS) AF: 0.117 AC: 564 AN: 4814

European-Finnish (FIN) AF: 0.0734 AC: 779 AN: 10608

Middle Eastern (MID) AF: 0.214 AC: 63 AN: 294

European-Non Finnish (NFE) AF: 0.119 AC: 8067 AN: 67984

Other (OTH) AF: 0.230 AC: 486 AN: 2110

Alfa AF: 0.198 Hom.: 891

Bravo AF: 0.270

Asia WGS AF: 0.120 AC: 418 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	2.4
DANN	Benign	0.73
PhyloP100		0.24

Splicing

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

Other links and lift over

dbSNP: rs2631878; hg19: chr8-21129059;