rs1882051

Variant names:

• chr7-36064656-T-A
• rs1882051
• ENST00000650410.1:n.-59T>A

Your query was ambiguous. Multiple possible variants found:

• chr7-36064656-T-A
• chr7-36064656-T-C
• chr7-36064656-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000650410.1(ENSG00000285573):​n.-59T>A variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.105 in 152,186 control chromosomes in the GnomAD database, including 1,166 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 0.11 (1166 hom., cov: 32)
• Consequence: ENSG00000285573 ENST00000650410.1 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.308

Genes affected

ENSG00000285573 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.154 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
ENSG00000285573	ENST00000650410.1	n.-59T>A		upstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.106 AC: 16049 AN: 152068 Hom.: 1166 Cov.: 32

Gnomad AFR AF: 0.0279

Gnomad AMI AF: 0.151

Gnomad AMR AF: 0.0976

Gnomad ASJ AF: 0.138

Gnomad EAS AF: 0.00116

Gnomad SAS AF: 0.0369

Gnomad FIN AF: 0.157

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.157

Gnomad OTH AF: 0.124

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

GnomAD4 genome AF: 0.105 AC: 16045 AN: 152186 Hom.: 1166 Cov.: 32 AF XY: 0.102 AC XY: 7625 AN XY: 74406

Gnomad4 AFR AF: 0.0278

Gnomad4 AMR AF: 0.0975

Gnomad4 ASJ AF: 0.138

Gnomad4 EAS AF: 0.00116

Gnomad4 SAS AF: 0.0369

Gnomad4 FIN AF: 0.157

Gnomad4 NFE AF: 0.157

Gnomad4 OTH AF: 0.122

Alfa AF: 0.0538 Hom.: 73

Bravo AF: 0.0982

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.7
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1882051; hg19: chr7-36104266;