3-138982345-C-G

Variant names:

• chr3-138982345-C-G
• rs360704

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.662 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

Gnomad4 AFR AF: 0.446

Gnomad4 AMR AF: 0.606

Gnomad4 ASJ AF: 0.825

Gnomad4 EAS AF: 0.641

Gnomad4 SAS AF: 0.739

Gnomad4 FIN AF: 0.781

Gnomad4 NFE AF: 0.772

Gnomad4 OTH AF: 0.669

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs360704; hg19: chr3-138701187;