9-117796733-T-C

Variant names:

• chr9-117796733-T-C
• rs10115586
• ENST00000697666.1:c.141-51332T>C

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000697666.1(ENSG00000285082):​c.141-51332T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.678 in 151,856 control chromosomes in the GnomAD database, including 35,431 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 0.68 (35431 hom., cov: 33)
• Consequence: ENSG00000285082 ENST00000697666.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.06
• Publications: 8 publications found

Genes affected

ENSG00000285082 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.22).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.967 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000697666.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000285082	ENST00000697666.1		c.141-51332T>C		intron	N/A	ENSP00000513391.1	A0A8V8TMK6
	ENSG00000285082	ENST00000646089.2		c.94-51332T>C		intron	N/A	ENSP00000496197.1	A0A2R8YGN2
	ENSG00000285082	ENST00000697637.1		c.94-51332T>C		intron	N/A	ENSP00000513367.1	A0A2R8YGN2

Frequencies

GnomAD3 genomes AF: 0.678 AC: 102905 AN: 151738 Hom.: 35403 Cov.: 33

Gnomad AFR AF: 0.609

Gnomad AMI AF: 0.748

Gnomad AMR AF: 0.715

Gnomad ASJ AF: 0.629

Gnomad EAS AF: 0.990

Gnomad SAS AF: 0.744

Gnomad FIN AF: 0.797

Gnomad MID AF: 0.598

Gnomad NFE AF: 0.667

Gnomad OTH AF: 0.674

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

GnomAD4 genome AF: 0.678 AC: 102983 AN: 151856 Hom.: 35431 Cov.: 33 AF XY: 0.688 AC XY: 51036 AN XY: 74188

African (AFR) AF: 0.609 AC: 25222 AN: 41434

American (AMR) AF: 0.715 AC: 10892 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.629 AC: 2179 AN: 3464

East Asian (EAS) AF: 0.990 AC: 5076 AN: 5126

South Asian (SAS) AF: 0.744 AC: 3585 AN: 4820

European-Finnish (FIN) AF: 0.797 AC: 8444 AN: 10594

Middle Eastern (MID) AF: 0.619 AC: 182 AN: 294

European-Non Finnish (NFE) AF: 0.667 AC: 45300 AN: 67874

Other (OTH) AF: 0.675 AC: 1421 AN: 2106

Alfa AF: 0.659 Hom.: 19061

Bravo AF: 0.673

Asia WGS AF: 0.846 AC: 2937 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.22
CADD	Benign	17
DANN	Benign	0.79
PhyloP100		3.1

Splicing

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

Other links and lift over

dbSNP: rs10115586; hg19: chr9-120559011;