3-186842019-C-T

Variant names:

• chr3-186842019-C-T
• rs76786086

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 0.0189 in 152,234 control chromosomes in the GnomAD database, including 50 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 0.019 (50 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.08
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0528 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: 0.0189 AC: 2882 AN: 152116 Hom.: 50 Cov.: 32

Gnomad AFR AF: 0.00391

Gnomad AMI AF: 0.0625

Gnomad AMR AF: 0.00780

Gnomad ASJ AF: 0.0147

Gnomad EAS AF: 0.0185

Gnomad SAS AF: 0.0585

Gnomad FIN AF: 0.0256

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.0266

Gnomad OTH AF: 0.0172

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

GnomAD4 genome AF: 0.0189 AC: 2882 AN: 152234 Hom.: 50 Cov.: 32 AF XY: 0.0197 AC XY: 1468 AN XY: 74430

African (AFR) AF: 0.00390 AC: 162 AN: 41548

American (AMR) AF: 0.00779 AC: 119 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0147 AC: 51 AN: 3472

East Asian (EAS) AF: 0.0185 AC: 96 AN: 5184

South Asian (SAS) AF: 0.0584 AC: 281 AN: 4814

European-Finnish (FIN) AF: 0.0256 AC: 272 AN: 10608

Middle Eastern (MID) AF: 0.00340 AC: 1 AN: 294

European-Non Finnish (NFE) AF: 0.0266 AC: 1806 AN: 68008

Other (OTH) AF: 0.0175 AC: 37 AN: 2112

Alfa AF: 0.0156 Hom.: 7

Bravo AF: 0.0158

Asia WGS AF: 0.0400 AC: 139 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	3.2
DANN	Benign	0.54
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs76786086; hg19: chr3-186559808;