9-86501713-G-C

Variant names:

• chr9-86501713-G-C
• rs8181166
• ENST00000739666.1:n.279-11740G>C

Variant summary

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

The ENST00000739666.1(ENSG00000235819):​n.279-11740G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.53 in 151,058 control chromosomes in the GnomAD database, including 22,244 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 0.53 (22244 hom., cov: 29)
• Consequence: ENSG00000235819 ENST00000739666.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.708
• Publications: 27 publications found

Genes affected

ENSG00000235819 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.939 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000739666.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000235819	ENST00000739666.1		n.279-11740G>C		intron	N/A
	ENSG00000235819	ENST00000739667.1		n.249-11740G>C		intron	N/A
	ENSG00000235819	ENST00000739668.1		n.327-11740G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.530 AC: 80009 AN: 150942 Hom.: 22231 Cov.: 29

Gnomad AFR AF: 0.461

Gnomad AMI AF: 0.393

Gnomad AMR AF: 0.614

Gnomad ASJ AF: 0.494

Gnomad EAS AF: 0.962

Gnomad SAS AF: 0.772

Gnomad FIN AF: 0.594

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.498

Gnomad OTH AF: 0.526

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

GnomAD4 genome AF: 0.530 AC: 80057 AN: 151058 Hom.: 22244 Cov.: 29 AF XY: 0.543 AC XY: 40077 AN XY: 73746

African (AFR) AF: 0.460 AC: 18946 AN: 41152

American (AMR) AF: 0.614 AC: 9333 AN: 15190

Ashkenazi Jewish (ASJ) AF: 0.494 AC: 1710 AN: 3464

East Asian (EAS) AF: 0.962 AC: 4929 AN: 5126

South Asian (SAS) AF: 0.772 AC: 3682 AN: 4770

European-Finnish (FIN) AF: 0.594 AC: 6117 AN: 10302

Middle Eastern (MID) AF: 0.507 AC: 149 AN: 294

European-Non Finnish (NFE) AF: 0.498 AC: 33730 AN: 67756

Other (OTH) AF: 0.527 AC: 1105 AN: 2098

Alfa AF: 0.928 Hom.: 33339

Bravo AF: 0.526

Asia WGS AF: 0.830 AC: 2880 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.69
DANN	Benign	0.32
PhyloP100		-0.71

Splicing

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

Other links and lift over

dbSNP: rs8181166; hg19: chr9-89116628;