8-127653235-C-T

Variant names:

• chr8-127653235-C-T
• rs4385433
• ENST00000754566.1:n.110+15479G>A

Variant summary

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

The ENST00000754566.1(ENSG00000286010):​n.110+15479G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.325 in 151,984 control chromosomes in the GnomAD database, including 8,591 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 0.33 (8591 hom., cov: 32)
• Consequence: ENSG00000286010 ENST00000754566.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.223
• Publications: 2 publications found

Genes affected

ENSG00000286010 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.394 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
ENSG00000286010	ENST00000754566.1	n.110+15479G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.325 AC: 49392 AN: 151866 Hom.: 8579 Cov.: 32

Gnomad AFR AF: 0.196

Gnomad AMI AF: 0.282

Gnomad AMR AF: 0.360

Gnomad ASJ AF: 0.322

Gnomad EAS AF: 0.381

Gnomad SAS AF: 0.409

Gnomad FIN AF: 0.402

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.375

Gnomad OTH AF: 0.321

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

GnomAD4 genome AF: 0.325 AC: 49445 AN: 151984 Hom.: 8591 Cov.: 32 AF XY: 0.326 AC XY: 24239 AN XY: 74298

African (AFR) AF: 0.196 AC: 8135 AN: 41434

American (AMR) AF: 0.361 AC: 5509 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.322 AC: 1116 AN: 3466

East Asian (EAS) AF: 0.380 AC: 1966 AN: 5168

South Asian (SAS) AF: 0.409 AC: 1967 AN: 4810

European-Finnish (FIN) AF: 0.402 AC: 4245 AN: 10550

Middle Eastern (MID) AF: 0.279 AC: 82 AN: 294

European-Non Finnish (NFE) AF: 0.375 AC: 25471 AN: 67960

Other (OTH) AF: 0.330 AC: 697 AN: 2112

Alfa AF: 0.352 Hom.: 19003

Bravo AF: 0.314

Asia WGS AF: 0.414 AC: 1436 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.84
DANN	Benign	0.47
PhyloP100		-0.22

Splicing

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

Other links and lift over

dbSNP: rs4385433; hg19: chr8-128665480;