rs10501784

Variant names:

• chr11-92219378-A-G
• rs10501784
• ENST00000837879.1:n.-1T>C

Variant summary

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

The ENST00000837879.1(ENSG00000309025):​n.-1T>C variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.787 in 152,172 control chromosomes in the GnomAD database, including 47,332 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 0.79 (47332 hom., cov: 33)
• Consequence: ENSG00000309025 ENST00000837879.1 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.237
• Publications: 4 publications found

Genes affected

ENSG00000309025 (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 (SAS) allele frequency at 95% confidence interval = 0.826 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000309025	ENST00000837879.1	n.-1T>C		upstream_gene_variant
ENSG00000309025	ENST00000837880.1	n.-42T>C		upstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.787 AC: 119721 AN: 152054 Hom.: 47284 Cov.: 33

Gnomad AFR AF: 0.812

Gnomad AMI AF: 0.866

Gnomad AMR AF: 0.837

Gnomad ASJ AF: 0.802

Gnomad EAS AF: 0.616

Gnomad SAS AF: 0.837

Gnomad FIN AF: 0.708

Gnomad MID AF: 0.844

Gnomad NFE AF: 0.781

Gnomad OTH AF: 0.789

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

GnomAD4 genome AF: 0.787 AC: 119827 AN: 152172 Hom.: 47332 Cov.: 33 AF XY: 0.784 AC XY: 58340 AN XY: 74368

African (AFR) AF: 0.812 AC: 33717 AN: 41542

American (AMR) AF: 0.838 AC: 12812 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.802 AC: 2783 AN: 3470

East Asian (EAS) AF: 0.617 AC: 3189 AN: 5172

South Asian (SAS) AF: 0.838 AC: 4037 AN: 4818

European-Finnish (FIN) AF: 0.708 AC: 7487 AN: 10578

Middle Eastern (MID) AF: 0.846 AC: 247 AN: 292

European-Non Finnish (NFE) AF: 0.781 AC: 53103 AN: 67990

Other (OTH) AF: 0.789 AC: 1662 AN: 2106

Alfa AF: 0.782 Hom.: 16723

Bravo AF: 0.795

Asia WGS AF: 0.742 AC: 2581 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	3.2
DANN	Benign	0.67
PhyloP100		0.24

Splicing

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

Other links and lift over

dbSNP: rs10501784; hg19: chr11-91952544;