3-186869628-T-C

Variant names:

• chr3-186869628-T-C
• rs9860747

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 0.705 in 152,220 control chromosomes in the GnomAD database, including 40,675 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 0.70 (40675 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.188
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.65).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.842 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: 0.705 AC: 107247 AN: 152104 Hom.: 40670 Cov.: 34

Gnomad AFR AF: 0.408

Gnomad AMI AF: 0.936

Gnomad AMR AF: 0.759

Gnomad ASJ AF: 0.762

Gnomad EAS AF: 0.594

Gnomad SAS AF: 0.839

Gnomad FIN AF: 0.826

Gnomad MID AF: 0.639

Gnomad NFE AF: 0.848

Gnomad OTH AF: 0.725

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

GnomAD4 genome AF: 0.705 AC: 107276 AN: 152220 Hom.: 40675 Cov.: 34 AF XY: 0.707 AC XY: 52599 AN XY: 74440

African (AFR) AF: 0.407 AC: 16907 AN: 41504

American (AMR) AF: 0.759 AC: 11605 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.762 AC: 2645 AN: 3472

East Asian (EAS) AF: 0.594 AC: 3077 AN: 5182

South Asian (SAS) AF: 0.841 AC: 4062 AN: 4830

European-Finnish (FIN) AF: 0.826 AC: 8757 AN: 10602

Middle Eastern (MID) AF: 0.639 AC: 188 AN: 294

European-Non Finnish (NFE) AF: 0.848 AC: 57651 AN: 68020

Other (OTH) AF: 0.724 AC: 1530 AN: 2114

Alfa AF: 0.750 Hom.: 11320

Bravo AF: 0.683

Asia WGS AF: 0.682 AC: 2374 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.65
CADD	Benign	8.8
DANN	Benign	0.81
PhyloP100		0.19

Splicing

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

Other links and lift over

dbSNP: rs9860747; hg19: chr3-186587417;