3-138928134-A-G

Variant names:

• chr3-138928134-A-G
• rs9857349

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 0.593 in 152,174 control chromosomes in the GnomAD database, including 28,195 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 0.59 (28195 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.247
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.961 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.593 AC: 90168 AN: 152056 Hom.: 28132 Cov.: 34

Gnomad AFR AF: 0.719

Gnomad AMI AF: 0.491

Gnomad AMR AF: 0.631

Gnomad ASJ AF: 0.489

Gnomad EAS AF: 0.983

Gnomad SAS AF: 0.579

Gnomad FIN AF: 0.672

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.475

Gnomad OTH AF: 0.544

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

GnomAD4 genome AF: 0.593 AC: 90290 AN: 152174 Hom.: 28195 Cov.: 34 AF XY: 0.605 AC XY: 45011 AN XY: 74388

African (AFR) AF: 0.720 AC: 29880 AN: 41508

American (AMR) AF: 0.632 AC: 9666 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.489 AC: 1698 AN: 3472

East Asian (EAS) AF: 0.983 AC: 5104 AN: 5190

South Asian (SAS) AF: 0.579 AC: 2797 AN: 4830

European-Finnish (FIN) AF: 0.672 AC: 7118 AN: 10592

Middle Eastern (MID) AF: 0.459 AC: 135 AN: 294

European-Non Finnish (NFE) AF: 0.475 AC: 32285 AN: 67972

Other (OTH) AF: 0.549 AC: 1159 AN: 2112

Alfa AF: 0.564 Hom.: 2756

Bravo AF: 0.600

Asia WGS AF: 0.806 AC: 2803 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	16
DANN	Benign	0.80
PhyloP100		0.25

Splicing

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

Other links and lift over

dbSNP: rs9857349; hg19: chr3-138646976;