rs13085499

Positions:

• chr3-186863051-G-A
• chr3-186863051-G-C

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 0.493 in 150,460 control chromosomes in the GnomAD database, including 18,574 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 0.49 (18574 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.41

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.09).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.546 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: 0.493 AC: 74141 AN: 150344 Hom.: 18568 Cov.: 29

Gnomad AFR AF: 0.417

Gnomad AMI AF: 0.593

Gnomad AMR AF: 0.452

Gnomad ASJ AF: 0.447

Gnomad EAS AF: 0.393

Gnomad SAS AF: 0.446

Gnomad FIN AF: 0.562

Gnomad MID AF: 0.415

Gnomad NFE AF: 0.551

Gnomad OTH AF: 0.458

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

GnomAD4 genome AF: 0.493 AC: 74176 AN: 150460 Hom.: 18574 Cov.: 29 AF XY: 0.491 AC XY: 35999 AN XY: 73368

Gnomad4 AFR AF: 0.416

Gnomad4 AMR AF: 0.452

Gnomad4 ASJ AF: 0.447

Gnomad4 EAS AF: 0.393

Gnomad4 SAS AF: 0.449

Gnomad4 FIN AF: 0.562

Gnomad4 NFE AF: 0.551

Gnomad4 OTH AF: 0.458

Alfa AF: 0.347 Hom.: 844

Bravo AF: 0.482

Asia WGS AF: 0.397 AC: 1380 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.60
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13085499; hg19: chr3-186580840;