rs581000

Positions:

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

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.76

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
		n.67684588C>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.657

Gnomad4 AMR AF: 0.810

Gnomad4 ASJ AF: 0.819

Gnomad4 EAS AF: 0.626

Gnomad4 SAS AF: 0.823

Gnomad4 FIN AF: 0.921

Gnomad4 NFE AF: 0.853

Gnomad4 OTH AF: 0.804

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs581000; hg19: chr1-68150271;