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: 74 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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105378010	XR_943010.2	n.-166G>A		upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000309813	ENST00000844074.1	n.-111G>A		upstream_gene_variant
ENSG00000309813	ENST00000844075.1	n.-138G>A		upstream_gene_variant
ENSG00000309813	ENST00000844076.1	n.-138G>A		upstream_gene_variant

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 v4.3

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

Other links and lift over

dbSNP: rs9402686; hg19: chr6-135427817; COSMIC: COSV73231460;