rs525960

Variant names:

• chr1-152525390-T-A
• rs525960

Your query was ambiguous. Multiple possible variants found:

• chr1-152525390-T-A
• chr1-152525390-T-C
• chr1-152525390-T-G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 7 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.225 AC: 9345 AN: 41468

American (AMR) AF: 0.548 AC: 8372 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.686 AC: 2381 AN: 3470

East Asian (EAS) AF: 0.645 AC: 3332 AN: 5162

South Asian (SAS) AF: 0.566 AC: 2727 AN: 4818

European-Finnish (FIN) AF: 0.746 AC: 7874 AN: 10554

Middle Eastern (MID) AF: 0.701 AC: 206 AN: 294

European-Non Finnish (NFE) AF: 0.635 AC: 43128 AN: 67916

Other (OTH) AF: 0.552 AC: 1164 AN: 2110

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	2.1
DANN	Benign	0.64
PhyloP100		-0.19

Splicing

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

Other links and lift over

dbSNP: rs525960; hg19: chr1-152497866;