rs6578592

Variant names:

• chr11-5247910-C-A
• rs6578592
• ENST00000759251.1:n.-203G>T

Your query was ambiguous. Multiple possible variants found:

• chr11-5247910-C-A
• chr11-5247910-C-G

Variant summary

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

The ENST00000759251.1(ENSG00000290652):​n.-203G>T variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.823 in 152,146 control chromosomes in the GnomAD database, including 51,752 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 0.82 (51752 hom., cov: 32)
• Consequence: ENSG00000290652 ENST00000759251.1 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0450
• Publications: 6 publications found

Genes affected

ENSG00000290652 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.884 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
ENSG00000290652	ENST00000759251.1	n.-203G>T		upstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.823 AC: 125073 AN: 152028 Hom.: 51694 Cov.: 32

Gnomad AFR AF: 0.891

Gnomad AMI AF: 0.757

Gnomad AMR AF: 0.850

Gnomad ASJ AF: 0.837

Gnomad EAS AF: 0.891

Gnomad SAS AF: 0.820

Gnomad FIN AF: 0.679

Gnomad MID AF: 0.842

Gnomad NFE AF: 0.791

Gnomad OTH AF: 0.846

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

GnomAD4 genome AF: 0.823 AC: 125193 AN: 152146 Hom.: 51752 Cov.: 32 AF XY: 0.818 AC XY: 60843 AN XY: 74360

African (AFR) AF: 0.891 AC: 37025 AN: 41536

American (AMR) AF: 0.850 AC: 13001 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.837 AC: 2905 AN: 3470

East Asian (EAS) AF: 0.891 AC: 4603 AN: 5164

South Asian (SAS) AF: 0.821 AC: 3957 AN: 4822

European-Finnish (FIN) AF: 0.679 AC: 7159 AN: 10540

Middle Eastern (MID) AF: 0.837 AC: 246 AN: 294

European-Non Finnish (NFE) AF: 0.791 AC: 53815 AN: 68004

Other (OTH) AF: 0.848 AC: 1792 AN: 2112

Alfa AF: 0.810 Hom.: 14938

Bravo AF: 0.838

Asia WGS AF: 0.862 AC: 2996 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.82
DANN	Benign	0.38
PhyloP100		-0.045

Splicing

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

Other links and lift over

dbSNP: rs6578592; hg19: chr11-5269140;