3-86156073-T-C

Variant names:

• chr3-86156073-T-C
• rs12636212

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 0.538 in 151,932 control chromosomes in the GnomAD database, including 22,338 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 0.54 (22338 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.205
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.572 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.538 AC: 81723 AN: 151814 Hom.: 22332 Cov.: 32

Gnomad AFR AF: 0.455

Gnomad AMI AF: 0.409

Gnomad AMR AF: 0.550

Gnomad ASJ AF: 0.493

Gnomad EAS AF: 0.519

Gnomad SAS AF: 0.444

Gnomad FIN AF: 0.680

Gnomad MID AF: 0.554

Gnomad NFE AF: 0.577

Gnomad OTH AF: 0.531

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

GnomAD4 genome AF: 0.538 AC: 81757 AN: 151932 Hom.: 22338 Cov.: 32 AF XY: 0.539 AC XY: 39988 AN XY: 74242

African (AFR) AF: 0.455 AC: 18837 AN: 41440

American (AMR) AF: 0.549 AC: 8376 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.493 AC: 1707 AN: 3462

East Asian (EAS) AF: 0.520 AC: 2675 AN: 5144

South Asian (SAS) AF: 0.442 AC: 2130 AN: 4814

European-Finnish (FIN) AF: 0.680 AC: 7177 AN: 10558

Middle Eastern (MID) AF: 0.558 AC: 164 AN: 294

European-Non Finnish (NFE) AF: 0.577 AC: 39204 AN: 67952

Other (OTH) AF: 0.529 AC: 1114 AN: 2104

Alfa AF: 0.562 Hom.: 19052

Bravo AF: 0.527

Asia WGS AF: 0.503 AC: 1752 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.3
DANN	Benign	0.73
PhyloP100		-0.20

Splicing

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

Other links and lift over

dbSNP: rs12636212; hg19: chr3-86205223;