rs7528484

chr1-24966177-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 0.473 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/exons	MANE	UniProt

Ensembl

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