chr9-117654894-T-G

Variant names:

• chr9-117654894-T-G
• rs12375686
• ENST00000450938.1:n.488-714T>G

Variant summary

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

The ENST00000450938.1(ENSG00000233569):​n.488-714T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.059 in 152,264 control chromosomes in the GnomAD database, including 333 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 0.059 (333 hom., cov: 32)
• Consequence: ENSG00000233569 ENST00000450938.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.624
• Publications: 2 publications found

Genes affected

ENSG00000233569 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.11 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000450938.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LOC101928797	NR_109806.1		n.488-714T>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000233569	ENST00000450938.1	TSL:1	n.488-714T>G		intron	N/A
	ENSG00000233569	ENST00000657171.1		n.486-714T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0591 AC: 8988 AN: 152146 Hom.: 334 Cov.: 32

Gnomad AFR AF: 0.0226

Gnomad AMI AF: 0.0373

Gnomad AMR AF: 0.0483

Gnomad ASJ AF: 0.0677

Gnomad EAS AF: 0.000964

Gnomad SAS AF: 0.118

Gnomad FIN AF: 0.0982

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0779

Gnomad OTH AF: 0.0550

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

GnomAD4 genome AF: 0.0590 AC: 8982 AN: 152264 Hom.: 333 Cov.: 32 AF XY: 0.0607 AC XY: 4518 AN XY: 74454

African (AFR) AF: 0.0225 AC: 937 AN: 41572

American (AMR) AF: 0.0482 AC: 737 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0677 AC: 235 AN: 3470

East Asian (EAS) AF: 0.000966 AC: 5 AN: 5176

South Asian (SAS) AF: 0.118 AC: 569 AN: 4824

European-Finnish (FIN) AF: 0.0982 AC: 1042 AN: 10608

Middle Eastern (MID) AF: 0.0408 AC: 12 AN: 294

European-Non Finnish (NFE) AF: 0.0779 AC: 5297 AN: 68002

Other (OTH) AF: 0.0540 AC: 114 AN: 2112

Alfa AF: 0.0674 Hom.: 73

Bravo AF: 0.0507

Asia WGS AF: 0.0680 AC: 235 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.62
DANN	Benign	0.68
PhyloP100		-0.62
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs12375686; hg19: chr9-120417172;