chr8-124281001-T-C

Variant names:

• chr8-124281001-T-C
• rs10808533
• ENST00000739901.1:n.297+4607T>C

Variant summary

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

The ENST00000739901.1(ENSG00000253227):​n.297+4607T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.66 in 152,100 control chromosomes in the GnomAD database, including 33,161 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 0.66 (33161 hom., cov: 33)
• Consequence: ENSG00000253227 ENST00000739901.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.135
• Publications: 8 publications found

Genes affected

ENSG00000253227 (HGNC:58365):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.729 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
ENSG00000253227	ENST00000739901.1	n.297+4607T>C		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.660 AC: 100289 AN: 151982 Hom.: 33116 Cov.: 33

Gnomad AFR AF: 0.665

Gnomad AMI AF: 0.702

Gnomad AMR AF: 0.695

Gnomad ASJ AF: 0.738

Gnomad EAS AF: 0.748

Gnomad SAS AF: 0.651

Gnomad FIN AF: 0.596

Gnomad MID AF: 0.646

Gnomad NFE AF: 0.648

Gnomad OTH AF: 0.667

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

GnomAD4 genome AF: 0.660 AC: 100382 AN: 152100 Hom.: 33161 Cov.: 33 AF XY: 0.659 AC XY: 49005 AN XY: 74364

African (AFR) AF: 0.665 AC: 27580 AN: 41478

American (AMR) AF: 0.695 AC: 10623 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.738 AC: 2561 AN: 3472

East Asian (EAS) AF: 0.749 AC: 3869 AN: 5168

South Asian (SAS) AF: 0.654 AC: 3157 AN: 4830

European-Finnish (FIN) AF: 0.596 AC: 6300 AN: 10568

Middle Eastern (MID) AF: 0.653 AC: 192 AN: 294

European-Non Finnish (NFE) AF: 0.648 AC: 44046 AN: 67978

Other (OTH) AF: 0.670 AC: 1414 AN: 2110

Alfa AF: 0.660 Hom.: 132337

Bravo AF: 0.671

Asia WGS AF: 0.695 AC: 2414 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	13
DANN	Benign	0.79
PhyloP100		-0.14

Splicing

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

Other links and lift over

dbSNP: rs10808533; hg19: chr8-125293242;