rs1258000

Variant names:

• chr1-46628595-C-T
• rs1258000

Variant summary

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

The variant allele was found at a frequency of 0.709 in 152,114 control chromosomes in the GnomAD database, including 38,421 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 0.71 (38421 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.182

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.754 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

Frequencies

GnomAD3 genomes AF: 0.709 AC: 107753 AN: 151996 Hom.: 38413 Cov.: 32

Gnomad AFR AF: 0.762

Gnomad AMI AF: 0.736

Gnomad AMR AF: 0.599

Gnomad ASJ AF: 0.633

Gnomad EAS AF: 0.615

Gnomad SAS AF: 0.721

Gnomad FIN AF: 0.727

Gnomad MID AF: 0.674

Gnomad NFE AF: 0.710

Gnomad OTH AF: 0.677

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

GnomAD4 genome AF: 0.709 AC: 107797 AN: 152114 Hom.: 38421 Cov.: 32 AF XY: 0.706 AC XY: 52488 AN XY: 74342

Gnomad4 AFR AF: 0.761

Gnomad4 AMR AF: 0.598

Gnomad4 ASJ AF: 0.633

Gnomad4 EAS AF: 0.615

Gnomad4 SAS AF: 0.720

Gnomad4 FIN AF: 0.727

Gnomad4 NFE AF: 0.709

Gnomad4 OTH AF: 0.676

Alfa AF: 0.710 Hom.: 17424

Bravo AF: 0.700

Asia WGS AF: 0.684 AC: 2378 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	7.7
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1258000; hg19: chr1-47094267; COSMIC: COSV64244040;