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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC102723490	XR_001749824.2	n.595-18446T>C		intron_variant	Intron 3 of 7
LOC102723490	XR_001749825.2	n.595-18446T>C		intron_variant	Intron 3 of 6
LOC102723490	XR_001749828.2	n.595-18446T>C		intron_variant	Intron 3 of 6
LOC102723490	XR_007063757.1	n.595-18446T>C		intron_variant	Intron 3 of 8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000294782	ENST00000725989.1	n.82+9804T>C		intron_variant	Intron 1 of 5

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 v4.3

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

Other links and lift over

dbSNP: rs9576104; hg19: chr13-37299292;