3-138982345-C-G

Variant names:

• chr3-138982345-C-G
• rs360704

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 0.661 in 151,860 control chromosomes in the GnomAD database, including 34,887 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 0.66 (34887 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.509
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.766 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.662 AC: 100388 AN: 151738 Hom.: 34870 Cov.: 30

Gnomad AFR AF: 0.446

Gnomad AMI AF: 0.772

Gnomad AMR AF: 0.606

Gnomad ASJ AF: 0.825

Gnomad EAS AF: 0.641

Gnomad SAS AF: 0.738

Gnomad FIN AF: 0.781

Gnomad MID AF: 0.791

Gnomad NFE AF: 0.772

Gnomad OTH AF: 0.674

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

GnomAD4 genome AF: 0.661 AC: 100427 AN: 151860 Hom.: 34887 Cov.: 30 AF XY: 0.663 AC XY: 49196 AN XY: 74216

African (AFR) AF: 0.446 AC: 18432 AN: 41364

American (AMR) AF: 0.606 AC: 9247 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.825 AC: 2864 AN: 3472

East Asian (EAS) AF: 0.641 AC: 3297 AN: 5146

South Asian (SAS) AF: 0.739 AC: 3546 AN: 4798

European-Finnish (FIN) AF: 0.781 AC: 8238 AN: 10548

Middle Eastern (MID) AF: 0.799 AC: 235 AN: 294

European-Non Finnish (NFE) AF: 0.772 AC: 52452 AN: 67952

Other (OTH) AF: 0.669 AC: 1412 AN: 2112

Alfa AF: 0.642 Hom.: 2130

Bravo AF: 0.639

Asia WGS AF: 0.632 AC: 2195 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	4.1
DANN	Benign	0.67
PhyloP100		-0.51

Splicing

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

Other links and lift over

dbSNP: rs360704; hg19: chr3-138701187;