5-85302499-G-T

Variant names:

• chr5-85302499-G-T
• rs4292478
• ENST00000730233.1:n.428-10956C>A

Variant summary

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

The ENST00000730233.1(ENSG00000295462):​n.428-10956C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.878 in 151,958 control chromosomes in the GnomAD database, including 58,893 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 0.88 (58893 hom., cov: 31)
• Consequence: ENSG00000295462 ENST00000730233.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.67
• Publications: 4 publications found

Genes affected

ENSG00000295462 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.905 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000730233.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000295462	ENST00000730233.1		n.428-10956C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.878 AC: 133373 AN: 151842 Hom.: 58846 Cov.: 31

Gnomad AFR AF: 0.912

Gnomad AMI AF: 0.943

Gnomad AMR AF: 0.819

Gnomad ASJ AF: 0.934

Gnomad EAS AF: 0.637

Gnomad SAS AF: 0.831

Gnomad FIN AF: 0.853

Gnomad MID AF: 0.877

Gnomad NFE AF: 0.893

Gnomad OTH AF: 0.869

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

GnomAD4 genome AF: 0.878 AC: 133478 AN: 151958 Hom.: 58893 Cov.: 31 AF XY: 0.873 AC XY: 64840 AN XY: 74278

African (AFR) AF: 0.912 AC: 37854 AN: 41490

American (AMR) AF: 0.819 AC: 12486 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.934 AC: 3237 AN: 3466

East Asian (EAS) AF: 0.637 AC: 3291 AN: 5164

South Asian (SAS) AF: 0.830 AC: 3998 AN: 4816

European-Finnish (FIN) AF: 0.853 AC: 8954 AN: 10502

Middle Eastern (MID) AF: 0.871 AC: 256 AN: 294

European-Non Finnish (NFE) AF: 0.893 AC: 60706 AN: 67950

Other (OTH) AF: 0.869 AC: 1836 AN: 2112

Alfa AF: 0.888 Hom.: 51943

Bravo AF: 0.878

Asia WGS AF: 0.760 AC: 2637 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.82
DANN	Benign	0.18
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs4292478; hg19: chr5-84598317;