ENST00000745587.1:n.137-4793A>G

Variant names:

• chr9-136965812-T-C
• rs11145951
• ENST00000745587.1:n.137-4793A>G

Variant summary

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

The ENST00000745587.1(ENSG00000297111):​n.137-4793A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.44 in 151,266 control chromosomes in the GnomAD database, including 15,798 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 0.44 (15798 hom., cov: 30)
• Consequence: ENSG00000297111 ENST00000745587.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.980
• Publications: 30 publications found

Genes affected

ENSG00000297111 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.512 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
ENSG00000297111	ENST00000745587.1	n.137-4793A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.440 AC: 66552 AN: 151184 Hom.: 15799 Cov.: 30

Gnomad AFR AF: 0.277

Gnomad AMI AF: 0.462

Gnomad AMR AF: 0.522

Gnomad ASJ AF: 0.466

Gnomad EAS AF: 0.175

Gnomad SAS AF: 0.429

Gnomad FIN AF: 0.589

Gnomad MID AF: 0.456

Gnomad NFE AF: 0.517

Gnomad OTH AF: 0.434

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

GnomAD4 genome AF: 0.440 AC: 66586 AN: 151266 Hom.: 15798 Cov.: 30 AF XY: 0.444 AC XY: 32779 AN XY: 73840

African (AFR) AF: 0.278 AC: 11432 AN: 41140

American (AMR) AF: 0.522 AC: 7936 AN: 15202

Ashkenazi Jewish (ASJ) AF: 0.466 AC: 1617 AN: 3470

East Asian (EAS) AF: 0.175 AC: 898 AN: 5124

South Asian (SAS) AF: 0.430 AC: 2060 AN: 4794

European-Finnish (FIN) AF: 0.589 AC: 6097 AN: 10356

Middle Eastern (MID) AF: 0.459 AC: 135 AN: 294

European-Non Finnish (NFE) AF: 0.517 AC: 35092 AN: 67884

Other (OTH) AF: 0.430 AC: 899 AN: 2092

Alfa AF: 0.489 Hom.: 64431

Bravo AF: 0.425

Asia WGS AF: 0.321 AC: 1118 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.5
DANN	Benign	0.16
PhyloP100		-0.98

Splicing

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

Other links and lift over

dbSNP: rs11145951; hg19: chr9-139860264;