rs312726

Variant names:

• chr17-70292187-C-A
• rs312726
• ENST00000771979.1:n.-223C>A

Your query was ambiguous. Multiple possible variants found:

• chr17-70292187-C-A
• chr17-70292187-C-G
• chr17-70292187-C-T

Variant summary

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

The ENST00000771979.1(ENSG00000300458):​n.-223C>A variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.763 in 151,936 control chromosomes in the GnomAD database, including 44,517 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 0.76 (44517 hom., cov: 31)
• Consequence: ENSG00000300458 ENST00000771979.1 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.313
• Publications: 7 publications found

Genes affected

ENSG00000300458 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.805 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
ENSG00000300458	ENST00000771979.1	n.-223C>A		upstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.763 AC: 115838 AN: 151818 Hom.: 44479 Cov.: 31

Gnomad AFR AF: 0.801

Gnomad AMI AF: 0.728

Gnomad AMR AF: 0.703

Gnomad ASJ AF: 0.692

Gnomad EAS AF: 0.530

Gnomad SAS AF: 0.826

Gnomad FIN AF: 0.836

Gnomad MID AF: 0.699

Gnomad NFE AF: 0.760

Gnomad OTH AF: 0.764

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

GnomAD4 genome AF: 0.763 AC: 115926 AN: 151936 Hom.: 44517 Cov.: 31 AF XY: 0.764 AC XY: 56763 AN XY: 74254

African (AFR) AF: 0.801 AC: 33166 AN: 41414

American (AMR) AF: 0.702 AC: 10711 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.692 AC: 2401 AN: 3472

East Asian (EAS) AF: 0.529 AC: 2729 AN: 5162

South Asian (SAS) AF: 0.826 AC: 3980 AN: 4816

European-Finnish (FIN) AF: 0.836 AC: 8813 AN: 10538

Middle Eastern (MID) AF: 0.701 AC: 206 AN: 294

European-Non Finnish (NFE) AF: 0.760 AC: 51647 AN: 67968

Other (OTH) AF: 0.764 AC: 1612 AN: 2110

Alfa AF: 0.756 Hom.: 19477

Bravo AF: 0.748

Asia WGS AF: 0.694 AC: 2413 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.3
DANN	Benign	0.34
PhyloP100		0.31

Splicing

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

Other links and lift over

dbSNP: rs312726; hg19: chr17-68288328;