rs9598025

Variant names:

• chr13-33723153-G-C
• rs9598025
• ENST00000731018.1:n.194+22758G>C

Variant summary

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

The ENST00000731018.1(ENSG00000295576):​n.194+22758G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0775 in 152,172 control chromosomes in the GnomAD database, including 999 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 0.078 (999 hom., cov: 32)
• Consequence: ENSG00000295576 ENST00000731018.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.874
• Publications: 1 publications found

Genes affected

ENSG00000295576 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.24 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000731018.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000295576	ENST00000731018.1		n.194+22758G>C		intron	N/A
	ENSG00000288767	ENST00000731141.1		n.51-38680G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0773 AC: 11758 AN: 152054 Hom.: 995 Cov.: 32

Gnomad AFR AF: 0.191

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0730

Gnomad ASJ AF: 0.0110

Gnomad EAS AF: 0.251

Gnomad SAS AF: 0.0512

Gnomad FIN AF: 0.0231

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0110

Gnomad OTH AF: 0.0641

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

GnomAD4 genome AF: 0.0775 AC: 11796 AN: 152172 Hom.: 999 Cov.: 32 AF XY: 0.0788 AC XY: 5863 AN XY: 74406

African (AFR) AF: 0.192 AC: 7955 AN: 41484

American (AMR) AF: 0.0733 AC: 1120 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0110 AC: 38 AN: 3470

East Asian (EAS) AF: 0.251 AC: 1300 AN: 5174

South Asian (SAS) AF: 0.0508 AC: 245 AN: 4824

European-Finnish (FIN) AF: 0.0231 AC: 245 AN: 10606

Middle Eastern (MID) AF: 0.0272 AC: 8 AN: 294

European-Non Finnish (NFE) AF: 0.0110 AC: 750 AN: 68008

Other (OTH) AF: 0.0634 AC: 134 AN: 2114

Alfa AF: 0.0457 Hom.: 65

Bravo AF: 0.0883

Asia WGS AF: 0.174 AC: 605 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.22
DANN	Benign	0.54
PhyloP100		-0.87

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs9598025;

hg19: chr13-34297290;