3-138835455-G-C

Variant names:

• chr3-138835455-G-C
• rs9289566

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 0.508 in 152,072 control chromosomes in the GnomAD database, including 22,176 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 0.51 (22176 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.98

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.742 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: 0.508 AC: 77186 AN: 151954 Hom.: 22141 Cov.: 33

Gnomad AFR AF: 0.748

Gnomad AMI AF: 0.497

Gnomad AMR AF: 0.388

Gnomad ASJ AF: 0.531

Gnomad EAS AF: 0.0154

Gnomad SAS AF: 0.343

Gnomad FIN AF: 0.335

Gnomad MID AF: 0.509

Gnomad NFE AF: 0.464

Gnomad OTH AF: 0.509

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

GnomAD4 genome AF: 0.508 AC: 77266 AN: 152072 Hom.: 22176 Cov.: 33 AF XY: 0.493 AC XY: 36629 AN XY: 74344

Gnomad4 AFR AF: 0.748

Gnomad4 AMR AF: 0.388

Gnomad4 ASJ AF: 0.531

Gnomad4 EAS AF: 0.0153

Gnomad4 SAS AF: 0.343

Gnomad4 FIN AF: 0.335

Gnomad4 NFE AF: 0.464

Gnomad4 OTH AF: 0.502

Alfa AF: 0.291 Hom.: 627

Bravo AF: 0.520

Asia WGS AF: 0.205 AC: 715 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.5
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9289566; hg19: chr3-138554297;