3-186867592-T-C

Variant names:

• chr3-186867592-T-C
• rs7628649

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 0.815 in 152,012 control chromosomes in the GnomAD database, including 51,196 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 0.81 (51196 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.29
• Publications: 15 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.887 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.815 AC: 123804 AN: 151894 Hom.: 51188 Cov.: 31

Gnomad AFR AF: 0.677

Gnomad AMI AF: 0.925

Gnomad AMR AF: 0.790

Gnomad ASJ AF: 0.793

Gnomad EAS AF: 0.695

Gnomad SAS AF: 0.866

Gnomad FIN AF: 0.927

Gnomad MID AF: 0.718

Gnomad NFE AF: 0.893

Gnomad OTH AF: 0.791

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

GnomAD4 genome AF: 0.815 AC: 123857 AN: 152012 Hom.: 51196 Cov.: 31 AF XY: 0.814 AC XY: 60498 AN XY: 74314

African (AFR) AF: 0.677 AC: 27991 AN: 41366

American (AMR) AF: 0.790 AC: 12073 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.793 AC: 2753 AN: 3470

East Asian (EAS) AF: 0.695 AC: 3597 AN: 5176

South Asian (SAS) AF: 0.867 AC: 4185 AN: 4826

European-Finnish (FIN) AF: 0.927 AC: 9802 AN: 10570

Middle Eastern (MID) AF: 0.728 AC: 214 AN: 294

European-Non Finnish (NFE) AF: 0.893 AC: 60731 AN: 68006

Other (OTH) AF: 0.789 AC: 1667 AN: 2112

Alfa AF: 0.861 Hom.: 117134

Bravo AF: 0.795

Asia WGS AF: 0.767 AC: 2667 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	6.9
DANN	Benign	0.52
PhyloP100		1.3

Splicing

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

Other links and lift over

dbSNP: rs7628649; hg19: chr3-186585381;