3-55447047-G-T

Variant names:

• chr3-55447047-G-T
• rs3913369

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 0.152 in 152,058 control chromosomes in the GnomAD database, including 2,344 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 0.15 (2344 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.65

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.227 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: 0.153 AC: 23184 AN: 151942 Hom.: 2345 Cov.: 32

Gnomad AFR AF: 0.0515

Gnomad AMI AF: 0.321

Gnomad AMR AF: 0.130

Gnomad ASJ AF: 0.151

Gnomad EAS AF: 0.00309

Gnomad SAS AF: 0.0731

Gnomad FIN AF: 0.177

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.230

Gnomad OTH AF: 0.171

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

GnomAD4 genome AF: 0.152 AC: 23175 AN: 152058 Hom.: 2344 Cov.: 32 AF XY: 0.147 AC XY: 10901 AN XY: 74308

Gnomad4 AFR AF: 0.0513

Gnomad4 AMR AF: 0.130

Gnomad4 ASJ AF: 0.151

Gnomad4 EAS AF: 0.00309

Gnomad4 SAS AF: 0.0725

Gnomad4 FIN AF: 0.177

Gnomad4 NFE AF: 0.230

Gnomad4 OTH AF: 0.170

Alfa AF: 0.177 Hom.: 1327

Bravo AF: 0.147

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.0030
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3913369; hg19: chr3-55481075;