3-138186011-A-G

Variant names:

• chr3-138186011-A-G
• rs329387

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 0.52 in 152,118 control chromosomes in the GnomAD database, including 21,477 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 0.52 (21477 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.30
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.793 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: 0.520 AC: 79073 AN: 152000 Hom.: 21467 Cov.: 33

Gnomad AFR AF: 0.384

Gnomad AMI AF: 0.475

Gnomad AMR AF: 0.616

Gnomad ASJ AF: 0.535

Gnomad EAS AF: 0.813

Gnomad SAS AF: 0.548

Gnomad FIN AF: 0.617

Gnomad MID AF: 0.455

Gnomad NFE AF: 0.542

Gnomad OTH AF: 0.526

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

GnomAD4 genome AF: 0.520 AC: 79119 AN: 152118 Hom.: 21477 Cov.: 33 AF XY: 0.527 AC XY: 39215 AN XY: 74364

African (AFR) AF: 0.384 AC: 15938 AN: 41488

American (AMR) AF: 0.616 AC: 9420 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.535 AC: 1856 AN: 3472

East Asian (EAS) AF: 0.814 AC: 4211 AN: 5176

South Asian (SAS) AF: 0.548 AC: 2642 AN: 4820

European-Finnish (FIN) AF: 0.617 AC: 6525 AN: 10578

Middle Eastern (MID) AF: 0.459 AC: 134 AN: 292

European-Non Finnish (NFE) AF: 0.542 AC: 36856 AN: 67986

Other (OTH) AF: 0.523 AC: 1105 AN: 2114

Alfa AF: 0.528 Hom.: 9218

Bravo AF: 0.520

Asia WGS AF: 0.663 AC: 2307 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	16
DANN	Benign	0.67
PhyloP100		1.3

Splicing

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

Other links and lift over

dbSNP: rs329387; hg19: chr3-137904853;