rs1525276

Variant names:

• chr3-180227563-C-A
• rs1525276

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 0.287 in 152,114 control chromosomes in the GnomAD database, including 6,491 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 0.29 (6491 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.154
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.462 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: 0.287 AC: 43629 AN: 151996 Hom.: 6483 Cov.: 33

Gnomad AFR AF: 0.331

Gnomad AMI AF: 0.310

Gnomad AMR AF: 0.349

Gnomad ASJ AF: 0.207

Gnomad EAS AF: 0.381

Gnomad SAS AF: 0.478

Gnomad FIN AF: 0.251

Gnomad MID AF: 0.275

Gnomad NFE AF: 0.235

Gnomad OTH AF: 0.287

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

GnomAD4 genome AF: 0.287 AC: 43671 AN: 152114 Hom.: 6491 Cov.: 33 AF XY: 0.294 AC XY: 21838 AN XY: 74358

African (AFR) AF: 0.331 AC: 13716 AN: 41486

American (AMR) AF: 0.350 AC: 5351 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.207 AC: 719 AN: 3470

East Asian (EAS) AF: 0.381 AC: 1970 AN: 5172

South Asian (SAS) AF: 0.478 AC: 2309 AN: 4826

European-Finnish (FIN) AF: 0.251 AC: 2649 AN: 10570

Middle Eastern (MID) AF: 0.276 AC: 81 AN: 294

European-Non Finnish (NFE) AF: 0.235 AC: 15987 AN: 67988

Other (OTH) AF: 0.288 AC: 607 AN: 2110

Alfa AF: 0.259 Hom.: 10821

Bravo AF: 0.292

Asia WGS AF: 0.438 AC: 1526 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.1
DANN	Benign	0.73
PhyloP100		-0.15

Splicing

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

Other links and lift over

dbSNP: rs1525276; hg19: chr3-179945351;