rs10118390

Variant names:

• chr9-104176474-C-T
• rs10118390
• ENST00000745188.1:n.710+27434G>A

Variant summary

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

The ENST00000745188.1(ENSG00000297079):​n.710+27434G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.122 in 151,910 control chromosomes in the GnomAD database, including 1,405 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 (1405 hom., cov: 32)
• Consequence: ENSG00000297079 ENST00000745188.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.47
• Publications: 1 publications found

Genes affected

ENSG00000297079 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.148 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
ENSG00000297079	ENST00000745188.1	n.710+27434G>A		intron_variant	Intron 5 of 8

Frequencies

GnomAD3 genomes AF: 0.122 AC: 18540 AN: 151792 Hom.: 1404 Cov.: 32

Gnomad AFR AF: 0.0720

Gnomad AMI AF: 0.236

Gnomad AMR AF: 0.0752

Gnomad ASJ AF: 0.138

Gnomad EAS AF: 0.0276

Gnomad SAS AF: 0.0875

Gnomad FIN AF: 0.252

Gnomad MID AF: 0.0924

Gnomad NFE AF: 0.151

Gnomad OTH AF: 0.113

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

GnomAD4 genome AF: 0.122 AC: 18558 AN: 151910 Hom.: 1405 Cov.: 32 AF XY: 0.123 AC XY: 9161 AN XY: 74230

African (AFR) AF: 0.0722 AC: 2997 AN: 41482

American (AMR) AF: 0.0751 AC: 1144 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.138 AC: 479 AN: 3466

East Asian (EAS) AF: 0.0277 AC: 142 AN: 5132

South Asian (SAS) AF: 0.0874 AC: 420 AN: 4808

European-Finnish (FIN) AF: 0.252 AC: 2657 AN: 10536

Middle Eastern (MID) AF: 0.0993 AC: 29 AN: 292

European-Non Finnish (NFE) AF: 0.151 AC: 10242 AN: 67946

Other (OTH) AF: 0.111 AC: 233 AN: 2096

Alfa AF: 0.146 Hom.: 252

Bravo AF: 0.104

Asia WGS AF: 0.0490 AC: 169 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.8
DANN	Benign	0.53
PhyloP100		-2.5

Splicing

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

Other links and lift over

dbSNP: rs10118390; hg19: chr9-106938755;