rs1523085

Variant names:

• chr3-145772585-G-A
• rs1523085

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 0.278 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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.280 AC: 11607 AN: 41434

American (AMR) AF: 0.257 AC: 3912 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.218 AC: 755 AN: 3470

East Asian (EAS) AF: 0.158 AC: 818 AN: 5170

South Asian (SAS) AF: 0.325 AC: 1561 AN: 4808

European-Finnish (FIN) AF: 0.311 AC: 3281 AN: 10556

Middle Eastern (MID) AF: 0.264 AC: 77 AN: 292

European-Non Finnish (NFE) AF: 0.286 AC: 19407 AN: 67960

Other (OTH) AF: 0.283 AC: 596 AN: 2106

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
PhyloP100		-0.27

Splicing

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

Other links and lift over

dbSNP: rs1523085; hg19: chr3-145490372;