rs1258000

chr1-46628595-C-T

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;