3-186781136-T-C

Position:

• chr3-186781136-T-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 0.835 in 152,252 control chromosomes in the GnomAD database, including 53,389 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 0.83 (53389 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.48

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.919 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.186781136T>C		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.835 AC: 126973 AN: 152134 Hom.: 53328 Cov.: 32

Gnomad AFR AF: 0.927

Gnomad AMI AF: 0.802

Gnomad AMR AF: 0.833

Gnomad ASJ AF: 0.766

Gnomad EAS AF: 0.905

Gnomad SAS AF: 0.785

Gnomad FIN AF: 0.842

Gnomad MID AF: 0.816

Gnomad NFE AF: 0.780

Gnomad OTH AF: 0.819

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

GnomAD4 genome AF: 0.835 AC: 127093 AN: 152252 Hom.: 53389 Cov.: 32 AF XY: 0.836 AC XY: 62234 AN XY: 74460

Gnomad4 AFR AF: 0.927

Gnomad4 AMR AF: 0.833

Gnomad4 ASJ AF: 0.766

Gnomad4 EAS AF: 0.905

Gnomad4 SAS AF: 0.785

Gnomad4 FIN AF: 0.842

Gnomad4 NFE AF: 0.780

Gnomad4 OTH AF: 0.822

Alfa AF: 0.806 Hom.: 10774

Bravo AF: 0.836

Asia WGS AF: 0.871 AC: 3028 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.51
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs266714; hg19: chr3-186498925;