ENST00000523678.1:n.124-27643C>A

Variant names:

• chr8-84016901-C-A
• rs62526245
• ENST00000523678.1:n.124-27643C>A

Variant summary

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

The ENST00000523678.1(ENSG00000254202):​n.124-27643C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.378 in 151,842 control chromosomes in the GnomAD database, including 11,775 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 0.38 (11775 hom., cov: 31)
• Consequence: ENSG00000254202 ENST00000523678.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.42
• Publications: 3 publications found

Genes affected

ENSG00000254202 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.573 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
ENSG00000254202	ENST00000523678.1	n.124-27643C>A		intron_variant	Intron 1 of 3	3

Frequencies

GnomAD3 genomes AF: 0.377 AC: 57243 AN: 151724 Hom.: 11743 Cov.: 31

Gnomad AFR AF: 0.535

Gnomad AMI AF: 0.175

Gnomad AMR AF: 0.331

Gnomad ASJ AF: 0.296

Gnomad EAS AF: 0.591

Gnomad SAS AF: 0.394

Gnomad FIN AF: 0.291

Gnomad MID AF: 0.299

Gnomad NFE AF: 0.296

Gnomad OTH AF: 0.353

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

GnomAD4 genome AF: 0.378 AC: 57338 AN: 151842 Hom.: 11775 Cov.: 31 AF XY: 0.380 AC XY: 28184 AN XY: 74222

African (AFR) AF: 0.536 AC: 22172 AN: 41396

American (AMR) AF: 0.330 AC: 5040 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.296 AC: 1025 AN: 3464

East Asian (EAS) AF: 0.591 AC: 3032 AN: 5130

South Asian (SAS) AF: 0.396 AC: 1902 AN: 4804

European-Finnish (FIN) AF: 0.291 AC: 3076 AN: 10554

Middle Eastern (MID) AF: 0.295 AC: 86 AN: 292

European-Non Finnish (NFE) AF: 0.296 AC: 20096 AN: 67932

Other (OTH) AF: 0.355 AC: 749 AN: 2108

Alfa AF: 0.332 Hom.: 1122

Bravo AF: 0.388

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.33
DANN	Benign	0.62
PhyloP100		-2.4

Splicing

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

Other links and lift over

dbSNP: rs62526245; hg19: chr8-84929136;