3-186502274-A-G

Variant names:

• chr3-186502274-A-G
• rs1868152

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 0.853 in 152,166 control chromosomes in the GnomAD database, including 55,576 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 0.85 (55576 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0750
• Publications: 13 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.897 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: 0.854 AC: 129778 AN: 152048 Hom.: 55544 Cov.: 31

Gnomad AFR AF: 0.789

Gnomad AMI AF: 0.930

Gnomad AMR AF: 0.884

Gnomad ASJ AF: 0.894

Gnomad EAS AF: 0.919

Gnomad SAS AF: 0.840

Gnomad FIN AF: 0.886

Gnomad MID AF: 0.924

Gnomad NFE AF: 0.874

Gnomad OTH AF: 0.855

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

GnomAD4 genome AF: 0.853 AC: 129858 AN: 152166 Hom.: 55576 Cov.: 31 AF XY: 0.855 AC XY: 63578 AN XY: 74396

African (AFR) AF: 0.788 AC: 32698 AN: 41474

American (AMR) AF: 0.885 AC: 13528 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.894 AC: 3101 AN: 3470

East Asian (EAS) AF: 0.919 AC: 4744 AN: 5162

South Asian (SAS) AF: 0.840 AC: 4053 AN: 4826

European-Finnish (FIN) AF: 0.886 AC: 9390 AN: 10602

Middle Eastern (MID) AF: 0.932 AC: 274 AN: 294

European-Non Finnish (NFE) AF: 0.874 AC: 59415 AN: 68018

Other (OTH) AF: 0.855 AC: 1809 AN: 2116

Alfa AF: 0.865 Hom.: 100927

Bravo AF: 0.854

Asia WGS AF: 0.885 AC: 3078 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	7.7
DANN	Benign	0.67
PhyloP100		-0.075

Splicing

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

Other links and lift over

dbSNP: rs1868152; hg19: chr3-186220063;