rs9402686

Variant names:

• chr6-135106679-G-A
• rs9402686
• ENST00000844074.1:n.-111G>A

Variant summary

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

The ENST00000844074.1(ENSG00000309813):​n.-111G>A variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.205 in 152,064 control chromosomes in the GnomAD database, including 3,956 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 0.21 (3956 hom., cov: 32)
• Consequence: ENSG00000309813 ENST00000844074.1 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.830
• Publications: 75 publications found

Genes affected

ENSG00000309813 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.268 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000844074.1. 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
	ENSG00000309813	ENST00000844074.1		n.-111G>A		upstream_gene	N/A
	ENSG00000309813	ENST00000844075.1		n.-138G>A		upstream_gene	N/A
	ENSG00000309813	ENST00000844076.1		n.-138G>A		upstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.205 AC: 31223 AN: 151946 Hom.: 3954 Cov.: 32

Gnomad AFR AF: 0.0720

Gnomad AMI AF: 0.190

Gnomad AMR AF: 0.193

Gnomad ASJ AF: 0.238

Gnomad EAS AF: 0.279

Gnomad SAS AF: 0.110

Gnomad FIN AF: 0.349

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.268

Gnomad OTH AF: 0.182

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

GnomAD4 genome AF: 0.205 AC: 31223 AN: 152064 Hom.: 3956 Cov.: 32 AF XY: 0.206 AC XY: 15293 AN XY: 74332

African (AFR) AF: 0.0719 AC: 2982 AN: 41484

American (AMR) AF: 0.193 AC: 2948 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.238 AC: 825 AN: 3470

East Asian (EAS) AF: 0.280 AC: 1447 AN: 5174

South Asian (SAS) AF: 0.110 AC: 530 AN: 4816

European-Finnish (FIN) AF: 0.349 AC: 3685 AN: 10564

Middle Eastern (MID) AF: 0.201 AC: 59 AN: 294

European-Non Finnish (NFE) AF: 0.268 AC: 18192 AN: 67956

Other (OTH) AF: 0.181 AC: 382 AN: 2114

Alfa AF: 0.254 Hom.: 16580

Bravo AF: 0.192

Asia WGS AF: 0.163 AC: 565 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	7.3
DANN	Benign	0.52
PhyloP100		0.83

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: rs9402686;

hg19: chr6-135427817;

COSMIC: COSV73231460;