ENST00000729573.1:n.486+858G>A

Variant names:

• chr4-8548118-C-T
• rs10805209
• ENST00000729573.1:n.486+858G>A

Variant summary

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

The ENST00000729573.1(ENSG00000295364):​n.486+858G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.309 in 152,140 control chromosomes in the GnomAD database, including 8,261 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 0.31 (8261 hom., cov: 33)
• Consequence: ENSG00000295364 ENST00000729573.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.732
• Publications: 4 publications found

Genes affected

ENSG00000295364 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.428 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000729573.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000295364	ENST00000729573.1		n.486+858G>A		intron	N/A
	ENSG00000295364	ENST00000729574.1		n.-138G>A		upstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.309 AC: 47041 AN: 152022 Hom.: 8256 Cov.: 33

Gnomad AFR AF: 0.150

Gnomad AMI AF: 0.334

Gnomad AMR AF: 0.332

Gnomad ASJ AF: 0.353

Gnomad EAS AF: 0.444

Gnomad SAS AF: 0.428

Gnomad FIN AF: 0.430

Gnomad MID AF: 0.309

Gnomad NFE AF: 0.362

Gnomad OTH AF: 0.302

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

GnomAD4 genome AF: 0.309 AC: 47081 AN: 152140 Hom.: 8261 Cov.: 33 AF XY: 0.315 AC XY: 23427 AN XY: 74380

African (AFR) AF: 0.150 AC: 6237 AN: 41538

American (AMR) AF: 0.332 AC: 5084 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.353 AC: 1223 AN: 3468

East Asian (EAS) AF: 0.443 AC: 2284 AN: 5154

South Asian (SAS) AF: 0.429 AC: 2066 AN: 4814

European-Finnish (FIN) AF: 0.430 AC: 4550 AN: 10584

Middle Eastern (MID) AF: 0.322 AC: 94 AN: 292

European-Non Finnish (NFE) AF: 0.362 AC: 24593 AN: 67966

Other (OTH) AF: 0.306 AC: 646 AN: 2110

Alfa AF: 0.348 Hom.: 39993

Bravo AF: 0.293

Asia WGS AF: 0.447 AC: 1551 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.5
DANN	Benign	0.18
PhyloP100		0.73

Splicing

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

Other links and lift over

dbSNP: rs10805209; hg19: chr4-8549845;