rs11789407

Variant names:

• chr9-118597268-C-A
• rs11789407
• ENST00000770012.1:n.-65G>T

Your query was ambiguous. Multiple possible variants found:

• chr9-118597268-C-A
• chr9-118597268-C-T

Variant summary

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

The ENST00000770012.1(ENSG00000300201):​n.-65G>T variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.433 in 151,976 control chromosomes in the GnomAD database, including 14,949 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 0.43 (14949 hom., cov: 32)
• Consequence: ENSG00000300201 ENST00000770012.1 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.309
• Publications: 8 publications found

Genes affected

ENSG00000300201 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.5 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105376249	XR_930297.2	n.-96G>T		upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000300201	ENST00000770012.1	n.-65G>T		upstream_gene_variant
ENSG00000300201	ENST00000770013.1	n.-62G>T		upstream_gene_variant
ENSG00000300201	ENST00000770014.1	n.-15G>T		upstream_gene_variant
ENSG00000300201	ENST00000770015.1	n.-63G>T		upstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.433 AC: 65682 AN: 151858 Hom.: 14937 Cov.: 32

Gnomad AFR AF: 0.340

Gnomad AMI AF: 0.514

Gnomad AMR AF: 0.396

Gnomad ASJ AF: 0.637

Gnomad EAS AF: 0.166

Gnomad SAS AF: 0.283

Gnomad FIN AF: 0.505

Gnomad MID AF: 0.440

Gnomad NFE AF: 0.504

Gnomad OTH AF: 0.464

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

GnomAD4 genome AF: 0.433 AC: 65736 AN: 151976 Hom.: 14949 Cov.: 32 AF XY: 0.428 AC XY: 31763 AN XY: 74280

African (AFR) AF: 0.341 AC: 14122 AN: 41472

American (AMR) AF: 0.396 AC: 6043 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.637 AC: 2209 AN: 3466

East Asian (EAS) AF: 0.166 AC: 859 AN: 5168

South Asian (SAS) AF: 0.282 AC: 1353 AN: 4806

European-Finnish (FIN) AF: 0.505 AC: 5335 AN: 10560

Middle Eastern (MID) AF: 0.429 AC: 126 AN: 294

European-Non Finnish (NFE) AF: 0.504 AC: 34250 AN: 67932

Other (OTH) AF: 0.460 AC: 970 AN: 2110

Alfa AF: 0.458 Hom.: 2817

Bravo AF: 0.420

Asia WGS AF: 0.249 AC: 869 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	4.7
DANN	Benign	0.74
PhyloP100		0.31

Splicing

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

Other links and lift over

dbSNP: rs11789407; hg19: chr9-121359546;