9-25612706-T-G

Variant names:

• chr9-25612706-T-G
• rs10511761
• ENST00000754095.1:n.224-4935T>G

Variant summary

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

The ENST00000754095.1(ENSG00000298250):​n.224-4935T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.516 in 152,048 control chromosomes in the GnomAD database, including 21,266 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 0.52 (21266 hom., cov: 32)
• Consequence: ENSG00000298250 ENST00000754095.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.847
• Publications: 5 publications found

Genes affected

ENSG00000298250 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.57).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.622 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
ENSG00000298250	ENST00000754095.1	n.224-4935T>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.516 AC: 78404 AN: 151932 Hom.: 21266 Cov.: 32

Gnomad AFR AF: 0.335

Gnomad AMI AF: 0.724

Gnomad AMR AF: 0.632

Gnomad ASJ AF: 0.571

Gnomad EAS AF: 0.552

Gnomad SAS AF: 0.540

Gnomad FIN AF: 0.539

Gnomad MID AF: 0.582

Gnomad NFE AF: 0.586

Gnomad OTH AF: 0.533

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

GnomAD4 genome AF: 0.516 AC: 78426 AN: 152048 Hom.: 21266 Cov.: 32 AF XY: 0.516 AC XY: 38330 AN XY: 74328

African (AFR) AF: 0.334 AC: 13876 AN: 41494

American (AMR) AF: 0.632 AC: 9647 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.571 AC: 1981 AN: 3472

East Asian (EAS) AF: 0.551 AC: 2850 AN: 5170

South Asian (SAS) AF: 0.538 AC: 2595 AN: 4822

European-Finnish (FIN) AF: 0.539 AC: 5693 AN: 10554

Middle Eastern (MID) AF: 0.582 AC: 171 AN: 294

European-Non Finnish (NFE) AF: 0.586 AC: 39828 AN: 67966

Other (OTH) AF: 0.533 AC: 1125 AN: 2110

Alfa AF: 0.560 Hom.: 73078

Bravo AF: 0.518

Asia WGS AF: 0.541 AC: 1879 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.57
CADD	Benign	17
DANN	Benign	0.57
PhyloP100		0.85

Splicing

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

Other links and lift over

dbSNP: rs10511761; hg19: chr9-25612704;