rs17705436

Variant names:

• chr9-6310908-C-G
• rs17705436
• ENST00000722750.1:n.102+17293G>C

Variant summary

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

The ENST00000722750.1(ENSG00000294323):​n.102+17293G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.165 in 152,134 control chromosomes in the GnomAD database, including 2,798 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 0.17 (2798 hom., cov: 32)
• Consequence: ENSG00000294323 ENST00000722750.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.553
• Publications: 8 publications found

Genes affected

ENSG00000294323 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.234 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000722750.1. 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
	ENSG00000294323	ENST00000722750.1		n.102+17293G>C		intron	N/A
	ENSG00000294323	ENST00000722751.1		n.103+17293G>C		intron	N/A
	ENSG00000294323	ENST00000722752.1		n.97-278G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.166 AC: 25162 AN: 152016 Hom.: 2799 Cov.: 32

Gnomad AFR AF: 0.0425

Gnomad AMI AF: 0.330

Gnomad AMR AF: 0.155

Gnomad ASJ AF: 0.245

Gnomad EAS AF: 0.000964

Gnomad SAS AF: 0.172

Gnomad FIN AF: 0.236

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.237

Gnomad OTH AF: 0.184

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

GnomAD4 genome AF: 0.165 AC: 25160 AN: 152134 Hom.: 2798 Cov.: 32 AF XY: 0.166 AC XY: 12318 AN XY: 74370

African (AFR) AF: 0.0423 AC: 1759 AN: 41544

American (AMR) AF: 0.155 AC: 2361 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.245 AC: 849 AN: 3468

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

South Asian (SAS) AF: 0.173 AC: 830 AN: 4804

European-Finnish (FIN) AF: 0.236 AC: 2497 AN: 10564

Middle Eastern (MID) AF: 0.163 AC: 48 AN: 294

European-Non Finnish (NFE) AF: 0.237 AC: 16124 AN: 67994

Other (OTH) AF: 0.183 AC: 386 AN: 2114

Alfa AF: 0.185 Hom.: 391

Bravo AF: 0.156

Asia WGS AF: 0.0590 AC: 208 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	1.2
DANN	Benign	0.81
PhyloP100		-0.55

Splicing

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

Other links and lift over

dbSNP: rs17705436; hg19: chr9-6310908;