3-186863051-G-A

Variant names:

• chr3-186863051-G-A
• rs13085499

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 0.493 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
• Publications: 6 publications found

ACMG classification

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

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.416 AC: 16948 AN: 40732

American (AMR) AF: 0.452 AC: 6810 AN: 15060

Ashkenazi Jewish (ASJ) AF: 0.447 AC: 1549 AN: 3462

East Asian (EAS) AF: 0.393 AC: 2000 AN: 5094

South Asian (SAS) AF: 0.449 AC: 2131 AN: 4748

European-Finnish (FIN) AF: 0.562 AC: 5784 AN: 10298

Middle Eastern (MID) AF: 0.422 AC: 124 AN: 294

European-Non Finnish (NFE) AF: 0.551 AC: 37339 AN: 67782

Other (OTH) AF: 0.458 AC: 957 AN: 2090

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
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs13085499; hg19: chr3-186580840;