rs13162612

Variant names:

• chr5-8042908-A-G
• rs13162612
• ENST00000723339.1:n.331-13606A>G

Variant summary

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

The ENST00000723339.1(ENSG00000294393):​n.331-13606A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0512 in 152,222 control chromosomes in the GnomAD database, including 216 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 0.051 (216 hom., cov: 32)
• Consequence: ENSG00000294393 ENST00000723339.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.377
• Publications: 3 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=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0628 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.331-13606A>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.0513 AC: 7806 AN: 152104 Hom.: 218 Cov.: 32

Gnomad AFR AF: 0.0203

Gnomad AMI AF: 0.0691

Gnomad AMR AF: 0.0625

Gnomad ASJ AF: 0.0407

Gnomad EAS AF: 0.0685

Gnomad SAS AF: 0.0560

Gnomad FIN AF: 0.0766

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.0625

Gnomad OTH AF: 0.0473

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

GnomAD4 genome AF: 0.0512 AC: 7801 AN: 152222 Hom.: 216 Cov.: 32 AF XY: 0.0523 AC XY: 3895 AN XY: 74410

African (AFR) AF: 0.0203 AC: 844 AN: 41546

American (AMR) AF: 0.0625 AC: 956 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0407 AC: 141 AN: 3468

East Asian (EAS) AF: 0.0687 AC: 355 AN: 5168

South Asian (SAS) AF: 0.0554 AC: 267 AN: 4818

European-Finnish (FIN) AF: 0.0766 AC: 812 AN: 10604

Middle Eastern (MID) AF: 0.0612 AC: 18 AN: 294

European-Non Finnish (NFE) AF: 0.0625 AC: 4248 AN: 68010

Other (OTH) AF: 0.0459 AC: 97 AN: 2114

Alfa AF: 0.0610 Hom.: 156

Bravo AF: 0.0485

Asia WGS AF: 0.0580 AC: 203 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.6
DANN	Benign	0.52
PhyloP100		-0.38

Splicing

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

Other links and lift over

dbSNP: rs13162612; hg19: chr5-8043021;