chr9-25449124-T-C

Variant names:

• chr9-25449124-T-C
• rs12552736
• ENST00000732866.1:n.119-26427A>G

Variant summary

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

The ENST00000732866.1(ENSG00000295812):​n.119-26427A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.115 in 152,132 control chromosomes in the GnomAD database, including 1,420 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 (1420 hom., cov: 32)
• Consequence: ENSG00000295812 ENST00000732866.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.753
• Publications: 13 publications found

Genes affected

ENSG00000295812 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.221 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
ENSG00000295812	ENST00000732866.1	n.119-26427A>G		intron_variant	Intron 1 of 4
ENSG00000295812	ENST00000732867.1	n.107+13476A>G		intron_variant	Intron 1 of 4
ENSG00000295812	ENST00000732868.1	n.95+13476A>G		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.115 AC: 17520 AN: 152014 Hom.: 1410 Cov.: 32

Gnomad AFR AF: 0.224

Gnomad AMI AF: 0.102

Gnomad AMR AF: 0.107

Gnomad ASJ AF: 0.0452

Gnomad EAS AF: 0.0172

Gnomad SAS AF: 0.0240

Gnomad FIN AF: 0.0628

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0776

Gnomad OTH AF: 0.0920

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

GnomAD4 genome AF: 0.115 AC: 17563 AN: 152132 Hom.: 1420 Cov.: 32 AF XY: 0.111 AC XY: 8286 AN XY: 74380

African (AFR) AF: 0.225 AC: 9327 AN: 41500

American (AMR) AF: 0.107 AC: 1633 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.0452 AC: 157 AN: 3470

East Asian (EAS) AF: 0.0172 AC: 89 AN: 5176

South Asian (SAS) AF: 0.0242 AC: 117 AN: 4830

European-Finnish (FIN) AF: 0.0628 AC: 665 AN: 10590

Middle Eastern (MID) AF: 0.0476 AC: 14 AN: 294

European-Non Finnish (NFE) AF: 0.0776 AC: 5276 AN: 67990

Other (OTH) AF: 0.0910 AC: 192 AN: 2110

Alfa AF: 0.0831 Hom.: 2005

Bravo AF: 0.126

Asia WGS AF: 0.0370 AC: 129 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.6
DANN	Benign	0.42
PhyloP100		-0.75

Splicing

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

Other links and lift over

dbSNP: rs12552736; hg19: chr9-25449122;