rs1523085

chr3-145772585-G-A

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 0.278 in 151,954 control chromosomes in the GnomAD database, including 5,960 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 0.28 (5960 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.269

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.311 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: 0.278 AC: 42254 AN: 151834 Hom.: 5953 Cov.: 33

Gnomad AFR AF: 0.281

Gnomad AMI AF: 0.288

Gnomad AMR AF: 0.257

Gnomad ASJ AF: 0.218

Gnomad EAS AF: 0.159

Gnomad SAS AF: 0.326

Gnomad FIN AF: 0.311

Gnomad MID AF: 0.255

Gnomad NFE AF: 0.286

Gnomad OTH AF: 0.278

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

GnomAD4 genome AF: 0.278 AC: 42277 AN: 151954 Hom.: 5960 Cov.: 33 AF XY: 0.280 AC XY: 20767 AN XY: 74240

Gnomad4 AFR AF: 0.280

Gnomad4 AMR AF: 0.257

Gnomad4 ASJ AF: 0.218

Gnomad4 EAS AF: 0.158

Gnomad4 SAS AF: 0.325

Gnomad4 FIN AF: 0.311

Gnomad4 NFE AF: 0.286

Gnomad4 OTH AF: 0.283

Alfa AF: 0.280 Hom.: 1384

Bravo AF: 0.272

Asia WGS AF: 0.267 AC: 928 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	0.42
Dann	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1523085; hg19: chr3-145490372;