chr1-152525390-T-A

Variant names:

• chr1-152525390-T-A
• rs525960

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 0.52 in 151,984 control chromosomes in the GnomAD database, including 23,063 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 0.52 (23063 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.187

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.63 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: 0.520 AC: 78969 AN: 151866 Hom.: 23044 Cov.: 32

Gnomad AFR AF: 0.225

Gnomad AMI AF: 0.531

Gnomad AMR AF: 0.547

Gnomad ASJ AF: 0.686

Gnomad EAS AF: 0.646

Gnomad SAS AF: 0.566

Gnomad FIN AF: 0.746

Gnomad MID AF: 0.696

Gnomad NFE AF: 0.635

Gnomad OTH AF: 0.546

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

GnomAD4 genome AF: 0.520 AC: 79013 AN: 151984 Hom.: 23063 Cov.: 32 AF XY: 0.527 AC XY: 39115 AN XY: 74274

Gnomad4 AFR AF: 0.225

Gnomad4 AMR AF: 0.548

Gnomad4 ASJ AF: 0.686

Gnomad4 EAS AF: 0.645

Gnomad4 SAS AF: 0.566

Gnomad4 FIN AF: 0.746

Gnomad4 NFE AF: 0.635

Gnomad4 OTH AF: 0.552

Alfa AF: 0.574 Hom.: 3361

Bravo AF: 0.493

Asia WGS AF: 0.573 AC: 1994 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	2.1
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs525960; hg19: chr1-152497866;