rs9314326

Variant names:

• chr8-26698878-C-T
• rs9314326
• ENST00000792407.1:n.85+28004C>T

Variant summary

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

The ENST00000792407.1(ENSG00000303169):​n.85+28004C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.199 in 152,056 control chromosomes in the GnomAD database, including 3,176 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 0.20 (3176 hom., cov: 33)
• Consequence: ENSG00000303169 ENST00000792407.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.219
• Publications: 0 publications found

Genes affected

ENSG00000303169 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.262 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000792407.1. 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
	ENSG00000303169	ENST00000792407.1		n.85+28004C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.199 AC: 30188 AN: 151936 Hom.: 3177 Cov.: 33

Gnomad AFR AF: 0.266

Gnomad AMI AF: 0.161

Gnomad AMR AF: 0.141

Gnomad ASJ AF: 0.142

Gnomad EAS AF: 0.249

Gnomad SAS AF: 0.114

Gnomad FIN AF: 0.184

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.180

Gnomad OTH AF: 0.159

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

GnomAD4 genome AF: 0.199 AC: 30210 AN: 152056 Hom.: 3176 Cov.: 33 AF XY: 0.195 AC XY: 14521 AN XY: 74302

African (AFR) AF: 0.266 AC: 11045 AN: 41490

American (AMR) AF: 0.141 AC: 2158 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.142 AC: 493 AN: 3470

East Asian (EAS) AF: 0.249 AC: 1286 AN: 5170

South Asian (SAS) AF: 0.113 AC: 542 AN: 4814

European-Finnish (FIN) AF: 0.184 AC: 1939 AN: 10540

Middle Eastern (MID) AF: 0.143 AC: 42 AN: 294

European-Non Finnish (NFE) AF: 0.180 AC: 12227 AN: 67968

Other (OTH) AF: 0.157 AC: 332 AN: 2112

Alfa AF: 0.202 Hom.: 425

Bravo AF: 0.199

Asia WGS AF: 0.169 AC: 589 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	7.4
DANN	Benign	0.34
PhyloP100		0.22

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs9314326;

hg19: chr8-26556395;