rs9347819

Variant names:

• chr6-164128680-C-T
• rs9347819
• ENST00000850151.1:n.311+69714C>T

Variant summary

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

The ENST00000850151.1(ENSG00000288696):​n.311+69714C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0728 in 152,158 control chromosomes in the GnomAD database, including 533 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 0.073 (533 hom., cov: 33)
• Consequence: ENSG00000288696 ENST00000850151.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.182
• Publications: 3 publications found

Genes affected

ENSG00000288696 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.133 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000850151.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000288696	ENST00000850151.1		n.311+69714C>T		intron	N/A
	ENSG00000288696	ENST00000850152.1		n.371+69714C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0727 AC: 11050 AN: 152040 Hom.: 529 Cov.: 33

Gnomad AFR AF: 0.115

Gnomad AMI AF: 0.0143

Gnomad AMR AF: 0.0806

Gnomad ASJ AF: 0.0721

Gnomad EAS AF: 0.142

Gnomad SAS AF: 0.130

Gnomad FIN AF: 0.0478

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0410

Gnomad OTH AF: 0.0674

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

GnomAD4 genome AF: 0.0728 AC: 11083 AN: 152158 Hom.: 533 Cov.: 33 AF XY: 0.0757 AC XY: 5635 AN XY: 74394

African (AFR) AF: 0.115 AC: 4767 AN: 41494

American (AMR) AF: 0.0811 AC: 1239 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0721 AC: 250 AN: 3466

East Asian (EAS) AF: 0.142 AC: 734 AN: 5170

South Asian (SAS) AF: 0.131 AC: 631 AN: 4814

European-Finnish (FIN) AF: 0.0478 AC: 506 AN: 10592

Middle Eastern (MID) AF: 0.0476 AC: 14 AN: 294

European-Non Finnish (NFE) AF: 0.0410 AC: 2789 AN: 68020

Other (OTH) AF: 0.0662 AC: 140 AN: 2114

Alfa AF: 0.0526 Hom.: 1163

Bravo AF: 0.0742

Asia WGS AF: 0.144 AC: 501 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	4.3
DANN	Benign	0.80
PhyloP100		-0.18

Splicing

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

Other links and lift over

dbSNP: rs9347819; hg19: chr6-164549712;