ENST00000517482.3:n.150+308G>A

Variant names:

• chr8-124272118-G-A
• rs4457311
• ENST00000517482.3:n.150+308G>A

Variant summary

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

The ENST00000517482.3(ENSG00000253227):​n.150+308G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.565 in 152,182 control chromosomes in the GnomAD database, including 24,550 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 0.56 (24550 hom., cov: 34)
• Consequence: ENSG00000253227 ENST00000517482.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.696
• Publications: 7 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=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.712 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000517482.3. 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
	ENSG00000253227	ENST00000517482.3	TSL:4	n.150+308G>A		intron	N/A
	ENSG00000253227	ENST00000660335.1		n.96+308G>A		intron	N/A
	ENSG00000253227	ENST00000668271.2		n.97+308G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.564 AC: 85834 AN: 152064 Hom.: 24513 Cov.: 34

Gnomad AFR AF: 0.591

Gnomad AMI AF: 0.475

Gnomad AMR AF: 0.583

Gnomad ASJ AF: 0.467

Gnomad EAS AF: 0.563

Gnomad SAS AF: 0.733

Gnomad FIN AF: 0.558

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.541

Gnomad OTH AF: 0.534

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

GnomAD4 genome AF: 0.565 AC: 85920 AN: 152182 Hom.: 24550 Cov.: 34 AF XY: 0.568 AC XY: 42284 AN XY: 74406

African (AFR) AF: 0.591 AC: 24533 AN: 41518

American (AMR) AF: 0.584 AC: 8920 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.467 AC: 1623 AN: 3472

East Asian (EAS) AF: 0.563 AC: 2913 AN: 5170

South Asian (SAS) AF: 0.732 AC: 3533 AN: 4824

European-Finnish (FIN) AF: 0.558 AC: 5912 AN: 10598

Middle Eastern (MID) AF: 0.480 AC: 141 AN: 294

European-Non Finnish (NFE) AF: 0.541 AC: 36775 AN: 68002

Other (OTH) AF: 0.539 AC: 1139 AN: 2114

Alfa AF: 0.548 Hom.: 68144

Bravo AF: 0.565

Asia WGS AF: 0.697 AC: 2420 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.50
DANN	Benign	0.76
PhyloP100		-0.70

Splicing

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

Other links and lift over

dbSNP: rs4457311; hg19: chr8-125284359;