rs7528484

Variant names:

• chr1-24966177-C-T
• rs7528484

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 0.473 in 152,102 control chromosomes in the GnomAD database, including 18,460 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 0.47 (18460 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.322

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.691 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: 0.473 AC: 71933 AN: 151984 Hom.: 18431 Cov.: 33

Gnomad AFR AF: 0.279

Gnomad AMI AF: 0.690

Gnomad AMR AF: 0.638

Gnomad ASJ AF: 0.510

Gnomad EAS AF: 0.710

Gnomad SAS AF: 0.671

Gnomad FIN AF: 0.575

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.500

Gnomad OTH AF: 0.508

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

GnomAD4 genome AF: 0.473 AC: 71981 AN: 152102 Hom.: 18460 Cov.: 33 AF XY: 0.488 AC XY: 36327 AN XY: 74372

Gnomad4 AFR AF: 0.279

Gnomad4 AMR AF: 0.639

Gnomad4 ASJ AF: 0.510

Gnomad4 EAS AF: 0.710

Gnomad4 SAS AF: 0.671

Gnomad4 FIN AF: 0.575

Gnomad4 NFE AF: 0.500

Gnomad4 OTH AF: 0.514

Alfa AF: 0.483 Hom.: 2301

Bravo AF: 0.470

Asia WGS AF: 0.692 AC: 2405 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	9.3
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7528484; hg19: chr1-25292668;