3-39544572-G-T

Variant names:

• chr3-39544572-G-T
• rs1513215

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 0.943 in 152,248 control chromosomes in the GnomAD database, including 67,906 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 0.94 (67906 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.14

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.964 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: 0.943 AC: 143533 AN: 152130 Hom.: 67851 Cov.: 31

Gnomad AFR AF: 0.902

Gnomad AMI AF: 0.993

Gnomad AMR AF: 0.959

Gnomad ASJ AF: 0.987

Gnomad EAS AF: 0.886

Gnomad SAS AF: 0.817

Gnomad FIN AF: 0.975

Gnomad MID AF: 0.956

Gnomad NFE AF: 0.970

Gnomad OTH AF: 0.949

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

GnomAD4 genome AF: 0.943 AC: 143643 AN: 152248 Hom.: 67906 Cov.: 31 AF XY: 0.941 AC XY: 70042 AN XY: 74444

Gnomad4 AFR AF: 0.902

Gnomad4 AMR AF: 0.959

Gnomad4 ASJ AF: 0.987

Gnomad4 EAS AF: 0.886

Gnomad4 SAS AF: 0.818

Gnomad4 FIN AF: 0.975

Gnomad4 NFE AF: 0.970

Gnomad4 OTH AF: 0.949

Alfa AF: 0.959 Hom.: 17027

Bravo AF: 0.943

Asia WGS AF: 0.840 AC: 2925 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	0.36
DANN	Benign	0.083

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1513215; hg19: chr3-39586063;