1-5251992-C-T

Variant names:

• chr1-5251992-C-T
• rs580309

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 0.454 in 151,794 control chromosomes in the GnomAD database, including 16,277 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 0.45 (16277 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.100

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.57 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: 0.453 AC: 68771 AN: 151678 Hom.: 16254 Cov.: 31

Gnomad AFR AF: 0.577

Gnomad AMI AF: 0.466

Gnomad AMR AF: 0.445

Gnomad ASJ AF: 0.393

Gnomad EAS AF: 0.217

Gnomad SAS AF: 0.322

Gnomad FIN AF: 0.352

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.426

Gnomad OTH AF: 0.457

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

GnomAD4 genome AF: 0.454 AC: 68845 AN: 151794 Hom.: 16277 Cov.: 31 AF XY: 0.445 AC XY: 32967 AN XY: 74152

Gnomad4 AFR AF: 0.577

Gnomad4 AMR AF: 0.444

Gnomad4 ASJ AF: 0.393

Gnomad4 EAS AF: 0.218

Gnomad4 SAS AF: 0.323

Gnomad4 FIN AF: 0.352

Gnomad4 NFE AF: 0.426

Gnomad4 OTH AF: 0.461

Alfa AF: 0.428 Hom.: 8594

Bravo AF: 0.465

Asia WGS AF: 0.270 AC: 943 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.8
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs580309; hg19: chr1-5312052;