chr6-119563679-G-A

Variant names:

• chr6-119563679-G-A
• rs9320695
• ENST00000692359.3:n.343+13284G>A

Variant summary

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

The ENST00000692359.3(ENSG00000287100):​n.343+13284G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.612 in 152,054 control chromosomes in the GnomAD database, including 29,673 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 0.61 (29673 hom., cov: 32)
• Consequence: ENSG00000287100 ENST00000692359.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.59
• Publications: 2 publications found

Genes affected

ENSG00000287100 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.69 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000692359.3. 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
	LOC105377975	NR_134600.1		n.252+13284G>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000287100	ENST00000692359.3		n.343+13284G>A		intron	N/A
	ENSG00000287100	ENST00000701050.2		n.328+13284G>A		intron	N/A
	ENSG00000287100	ENST00000701673.1		n.313+13280G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.612 AC: 93037 AN: 151936 Hom.: 29648 Cov.: 32

Gnomad AFR AF: 0.429

Gnomad AMI AF: 0.742

Gnomad AMR AF: 0.682

Gnomad ASJ AF: 0.643

Gnomad EAS AF: 0.483

Gnomad SAS AF: 0.689

Gnomad FIN AF: 0.700

Gnomad MID AF: 0.680

Gnomad NFE AF: 0.695

Gnomad OTH AF: 0.625

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

GnomAD4 genome AF: 0.612 AC: 93103 AN: 152054 Hom.: 29673 Cov.: 32 AF XY: 0.614 AC XY: 45679 AN XY: 74336

African (AFR) AF: 0.429 AC: 17761 AN: 41432

American (AMR) AF: 0.682 AC: 10425 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.643 AC: 2234 AN: 3472

East Asian (EAS) AF: 0.483 AC: 2500 AN: 5172

South Asian (SAS) AF: 0.689 AC: 3327 AN: 4826

European-Finnish (FIN) AF: 0.700 AC: 7398 AN: 10572

Middle Eastern (MID) AF: 0.680 AC: 200 AN: 294

European-Non Finnish (NFE) AF: 0.695 AC: 47252 AN: 67976

Other (OTH) AF: 0.629 AC: 1329 AN: 2112

Alfa AF: 0.642 Hom.: 5530

Bravo AF: 0.602

Asia WGS AF: 0.616 AC: 2142 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.070
DANN	Benign	0.29
PhyloP100		-3.6

Splicing

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

Other links and lift over

dbSNP: rs9320695; hg19: chr6-119884844;