rs581000

Variant names:

• chr1-67684588-C-G
• rs581000
• ENST00000790841.1:n.470G>C

Your query was ambiguous. Multiple possible variants found:

• chr1-67684588-C-G
• chr1-67684588-C-T

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000790841.1(ENSG00000302977):​n.470G>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.79 in 152,096 control chromosomes in the GnomAD database, including 48,231 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 (48231 hom., cov: 31)
• Consequence: ENSG00000302977 ENST00000790841.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.76
• Publications: 12 publications found

Genes affected

ENSG00000302977 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.38).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.848 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
ENSG00000302977	ENST00000790841.1	n.470G>C		non_coding_transcript_exon_variant	Exon 1 of 1

Frequencies

GnomAD3 genomes AF: 0.790 AC: 120102 AN: 151978 Hom.: 48199 Cov.: 31

Gnomad AFR AF: 0.657

Gnomad AMI AF: 0.874

Gnomad AMR AF: 0.810

Gnomad ASJ AF: 0.819

Gnomad EAS AF: 0.627

Gnomad SAS AF: 0.822

Gnomad FIN AF: 0.921

Gnomad MID AF: 0.775

Gnomad NFE AF: 0.854

Gnomad OTH AF: 0.803

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

GnomAD4 genome AF: 0.790 AC: 120190 AN: 152096 Hom.: 48231 Cov.: 31 AF XY: 0.791 AC XY: 58801 AN XY: 74338

African (AFR) AF: 0.657 AC: 27231 AN: 41432

American (AMR) AF: 0.810 AC: 12389 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.819 AC: 2837 AN: 3466

East Asian (EAS) AF: 0.626 AC: 3237 AN: 5170

South Asian (SAS) AF: 0.823 AC: 3958 AN: 4810

European-Finnish (FIN) AF: 0.921 AC: 9768 AN: 10602

Middle Eastern (MID) AF: 0.776 AC: 228 AN: 294

European-Non Finnish (NFE) AF: 0.853 AC: 58048 AN: 68012

Other (OTH) AF: 0.804 AC: 1697 AN: 2110

Alfa AF: 0.830 Hom.: 6243

Bravo AF: 0.773

Asia WGS AF: 0.743 AC: 2588 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.38
CADD	Benign	15
DANN	Benign	0.66
PhyloP100		1.8

Splicing

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

Other links and lift over

dbSNP: rs581000; hg19: chr1-68150271;