rs1519529

Variant names:

• chr2-136216687-C-G
• rs1519529

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 0.174 in 152,196 control chromosomes in the GnomAD database, including 3,130 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 0.17 (3130 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.179

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.254 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: 0.174 AC: 26459 AN: 152078 Hom.: 3129 Cov.: 32

Gnomad AFR AF: 0.0497

Gnomad AMI AF: 0.359

Gnomad AMR AF: 0.175

Gnomad ASJ AF: 0.185

Gnomad EAS AF: 0.00269

Gnomad SAS AF: 0.265

Gnomad FIN AF: 0.146

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.257

Gnomad OTH AF: 0.180

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

GnomAD4 genome AF: 0.174 AC: 26459 AN: 152196 Hom.: 3130 Cov.: 32 AF XY: 0.170 AC XY: 12621 AN XY: 74410

Gnomad4 AFR AF: 0.0495

Gnomad4 AMR AF: 0.175

Gnomad4 ASJ AF: 0.185

Gnomad4 EAS AF: 0.00270

Gnomad4 SAS AF: 0.266

Gnomad4 FIN AF: 0.146

Gnomad4 NFE AF: 0.257

Gnomad4 OTH AF: 0.178

Alfa AF: 0.190 Hom.: 440

Bravo AF: 0.166

Asia WGS AF: 0.105 AC: 363 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.8
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1519529; hg19: chr2-136974257;