5-89893319-G-A

Variant names:

• chr5-89893319-G-A
• rs12515716
• ENST00000740242.1:n.150+15633C>T

Variant summary

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

The ENST00000740242.1(ENSG00000296543):​n.150+15633C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.122 in 151,986 control chromosomes in the GnomAD database, including 1,344 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 0.12 (1344 hom., cov: 32)
• Consequence: ENSG00000296543 ENST00000740242.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.365
• Publications: 1 publications found

Genes affected

ENSG00000296543 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.203 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000740242.1. 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
	ENSG00000296543	ENST00000740242.1		n.150+15633C>T		intron	N/A
	ENSG00000214942	ENST00000740368.1		n.82+4185G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.122 AC: 18525 AN: 151870 Hom.: 1341 Cov.: 32

Gnomad AFR AF: 0.0825

Gnomad AMI AF: 0.0822

Gnomad AMR AF: 0.209

Gnomad ASJ AF: 0.274

Gnomad EAS AF: 0.152

Gnomad SAS AF: 0.123

Gnomad FIN AF: 0.0733

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.123

Gnomad OTH AF: 0.158

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

GnomAD4 genome AF: 0.122 AC: 18535 AN: 151986 Hom.: 1344 Cov.: 32 AF XY: 0.123 AC XY: 9109 AN XY: 74296

African (AFR) AF: 0.0825 AC: 3420 AN: 41466

American (AMR) AF: 0.209 AC: 3187 AN: 15226

Ashkenazi Jewish (ASJ) AF: 0.274 AC: 951 AN: 3472

East Asian (EAS) AF: 0.151 AC: 783 AN: 5172

South Asian (SAS) AF: 0.124 AC: 597 AN: 4816

European-Finnish (FIN) AF: 0.0733 AC: 775 AN: 10566

Middle Eastern (MID) AF: 0.218 AC: 64 AN: 294

European-Non Finnish (NFE) AF: 0.123 AC: 8353 AN: 67956

Other (OTH) AF: 0.157 AC: 330 AN: 2106

Alfa AF: 0.110 Hom.: 136

Bravo AF: 0.130

Asia WGS AF: 0.146 AC: 508 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.7
DANN	Benign	0.56
PhyloP100		0.36

Splicing

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

Other links and lift over

dbSNP: rs12515716; hg19: chr5-89189136;