3-15253857-A-G

Position:

• chr3-15253857-A-G

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 0.249 in 152,130 control chromosomes in the GnomAD database, including 6,922 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 0.25 (6922 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.92

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.49 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.248 AC: 37773 AN: 152012 Hom.: 6888 Cov.: 32

Gnomad AFR AF: 0.496

Gnomad AMI AF: 0.134

Gnomad AMR AF: 0.227

Gnomad ASJ AF: 0.0735

Gnomad EAS AF: 0.424

Gnomad SAS AF: 0.240

Gnomad FIN AF: 0.0902

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.126

Gnomad OTH AF: 0.229

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

GnomAD4 genome AF: 0.249 AC: 37853 AN: 152130 Hom.: 6922 Cov.: 32 AF XY: 0.248 AC XY: 18459 AN XY: 74382

Gnomad4 AFR AF: 0.496

Gnomad4 AMR AF: 0.228

Gnomad4 ASJ AF: 0.0735

Gnomad4 EAS AF: 0.423

Gnomad4 SAS AF: 0.240

Gnomad4 FIN AF: 0.0902

Gnomad4 NFE AF: 0.126

Gnomad4 OTH AF: 0.235

Alfa AF: 0.151 Hom.: 4560

Bravo AF: 0.271

Asia WGS AF: 0.375 AC: 1302 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.42
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1318937; hg19: chr3-15295364;