5-8047430-C-A

Variant names:

• chr5-8047430-C-A
• rs876712
• ENST00000723339.1:n.331-9084C>A

Variant summary

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

The ENST00000723339.1(ENSG00000294393):​n.331-9084C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.13 in 152,114 control chromosomes in the GnomAD database, including 1,739 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 0.13 (1739 hom., cov: 32)
• Consequence: ENSG00000294393 ENST00000723339.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.324
• Publications: 2 publications found

Genes affected

ENSG00000294393 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.25 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
ENSG00000294393	ENST00000723339.1	n.331-9084C>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.129 AC: 19679 AN: 151996 Hom.: 1734 Cov.: 32

Gnomad AFR AF: 0.254

Gnomad AMI AF: 0.0504

Gnomad AMR AF: 0.124

Gnomad ASJ AF: 0.0481

Gnomad EAS AF: 0.169

Gnomad SAS AF: 0.105

Gnomad FIN AF: 0.0224

Gnomad MID AF: 0.153

Gnomad NFE AF: 0.0753

Gnomad OTH AF: 0.124

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

GnomAD4 genome AF: 0.130 AC: 19699 AN: 152114 Hom.: 1739 Cov.: 32 AF XY: 0.128 AC XY: 9547 AN XY: 74366

African (AFR) AF: 0.254 AC: 10547 AN: 41466

American (AMR) AF: 0.124 AC: 1897 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0481 AC: 167 AN: 3472

East Asian (EAS) AF: 0.169 AC: 874 AN: 5174

South Asian (SAS) AF: 0.105 AC: 507 AN: 4820

European-Finnish (FIN) AF: 0.0224 AC: 237 AN: 10598

Middle Eastern (MID) AF: 0.140 AC: 41 AN: 292

European-Non Finnish (NFE) AF: 0.0753 AC: 5121 AN: 67980

Other (OTH) AF: 0.124 AC: 262 AN: 2114

Alfa AF: 0.0903 Hom.: 3648

Bravo AF: 0.143

Asia WGS AF: 0.175 AC: 607 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.60
DANN	Benign	0.29
PhyloP100		-0.32

Splicing

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

Other links and lift over

dbSNP: rs876712; hg19: chr5-8047543;