rs9592004

Variant names:

• chr13-33723567-A-G
• rs9592004
• ENST00000731018.1:n.194+23172A>G

Variant summary

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

The ENST00000731018.1(ENSG00000295576):​n.194+23172A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0772 in 152,270 control chromosomes in the GnomAD database, including 990 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 0.077 (990 hom., cov: 33)
• Consequence: ENSG00000295576 ENST00000731018.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.142
• 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=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.238 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

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
	ENSG00000295576	ENST00000731018.1		n.194+23172A>G		intron	N/A
	ENSG00000288767	ENST00000731141.1		n.51-38266A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0770 AC: 11720 AN: 152150 Hom.: 986 Cov.: 33

Gnomad AFR AF: 0.191

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0727

Gnomad ASJ AF: 0.0109

Gnomad EAS AF: 0.250

Gnomad SAS AF: 0.0510

Gnomad FIN AF: 0.0230

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0111

Gnomad OTH AF: 0.0641

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

GnomAD4 genome AF: 0.0772 AC: 11758 AN: 152270 Hom.: 990 Cov.: 33 AF XY: 0.0785 AC XY: 5846 AN XY: 74464

African (AFR) AF: 0.191 AC: 7928 AN: 41532

American (AMR) AF: 0.0730 AC: 1117 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.0109 AC: 38 AN: 3472

East Asian (EAS) AF: 0.250 AC: 1291 AN: 5172

South Asian (SAS) AF: 0.0506 AC: 244 AN: 4824

European-Finnish (FIN) AF: 0.0230 AC: 244 AN: 10618

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

European-Non Finnish (NFE) AF: 0.0111 AC: 753 AN: 68032

Other (OTH) AF: 0.0634 AC: 134 AN: 2112

Alfa AF: 0.0508 Hom.: 77

Bravo AF: 0.0879

Asia WGS AF: 0.175 AC: 606 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	3.2
DANN	Benign	0.65
PhyloP100		-0.14

Splicing

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

Other links and lift over

dbSNP: rs9592004; hg19: chr13-34297704;