chr3-186537043-A-G

Position:

• chr3-186537043-A-G

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 0.212 in 152,134 control chromosomes in the GnomAD database, including 4,072 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 0.21 (4072 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.458

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.341 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.212 AC: 32267 AN: 152016 Hom.: 4064 Cov.: 32

Gnomad AFR AF: 0.346

Gnomad AMI AF: 0.0504

Gnomad AMR AF: 0.204

Gnomad ASJ AF: 0.190

Gnomad EAS AF: 0.133

Gnomad SAS AF: 0.231

Gnomad FIN AF: 0.203

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.142

Gnomad OTH AF: 0.221

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

GnomAD4 genome AF: 0.212 AC: 32295 AN: 152134 Hom.: 4072 Cov.: 32 AF XY: 0.215 AC XY: 16005 AN XY: 74364

Gnomad4 AFR AF: 0.346

Gnomad4 AMR AF: 0.204

Gnomad4 ASJ AF: 0.190

Gnomad4 EAS AF: 0.133

Gnomad4 SAS AF: 0.230

Gnomad4 FIN AF: 0.203

Gnomad4 NFE AF: 0.142

Gnomad4 OTH AF: 0.220

Alfa AF: 0.160 Hom.: 4439

Bravo AF: 0.217

Asia WGS AF: 0.197 AC: 683 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	14
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1447670; hg19: chr3-186254832;