rs9576104

Variant names:

• chr13-36725155-A-G
• rs9576104
• ENST00000725989.1:n.82+9804T>C

Variant summary

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

The ENST00000725989.1(ENSG00000294782):​n.82+9804T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.118 in 152,074 control chromosomes in the GnomAD database, including 1,376 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 (1376 hom., cov: 31)
• Consequence: ENSG00000294782 ENST00000725989.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.852
• Publications: 1 publications found

Genes affected

ENSG00000294782 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.271 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000725989.1. 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
	ENSG00000294782	ENST00000725989.1		n.82+9804T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.118 AC: 17918 AN: 151956 Hom.: 1374 Cov.: 31

Gnomad AFR AF: 0.0376

Gnomad AMI AF: 0.0691

Gnomad AMR AF: 0.100

Gnomad ASJ AF: 0.102

Gnomad EAS AF: 0.272

Gnomad SAS AF: 0.283

Gnomad FIN AF: 0.170

Gnomad MID AF: 0.0478

Gnomad NFE AF: 0.142

Gnomad OTH AF: 0.100

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

GnomAD4 genome AF: 0.118 AC: 17926 AN: 152074 Hom.: 1376 Cov.: 31 AF XY: 0.123 AC XY: 9160 AN XY: 74332

African (AFR) AF: 0.0376 AC: 1560 AN: 41524

American (AMR) AF: 0.100 AC: 1531 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.102 AC: 353 AN: 3472

East Asian (EAS) AF: 0.272 AC: 1406 AN: 5162

South Asian (SAS) AF: 0.283 AC: 1362 AN: 4812

European-Finnish (FIN) AF: 0.170 AC: 1796 AN: 10556

Middle Eastern (MID) AF: 0.0445 AC: 13 AN: 292

European-Non Finnish (NFE) AF: 0.142 AC: 9625 AN: 67970

Other (OTH) AF: 0.103 AC: 217 AN: 2106

Alfa AF: 0.129 Hom.: 173

Bravo AF: 0.104

Asia WGS AF: 0.242 AC: 844 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	5.3
DANN	Benign	0.85
PhyloP100		0.85

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: rs9576104;

hg19: chr13-37299292;