3-145463083-C-T

Variant names:

• chr3-145463083-C-T
• rs708482

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 0.133 in 151,924 control chromosomes in the GnomAD database, including 1,444 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 0.13 (1444 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0760

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.158 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: 0.134 AC: 20276 AN: 151806 Hom.: 1447 Cov.: 29

Gnomad AFR AF: 0.0792

Gnomad AMI AF: 0.0504

Gnomad AMR AF: 0.131

Gnomad ASJ AF: 0.200

Gnomad EAS AF: 0.141

Gnomad SAS AF: 0.163

Gnomad FIN AF: 0.137

Gnomad MID AF: 0.261

Gnomad NFE AF: 0.161

Gnomad OTH AF: 0.150

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

GnomAD4 genome AF: 0.133 AC: 20268 AN: 151924 Hom.: 1444 Cov.: 29 AF XY: 0.133 AC XY: 9880 AN XY: 74232

Gnomad4 AFR AF: 0.0790

Gnomad4 AMR AF: 0.131

Gnomad4 ASJ AF: 0.200

Gnomad4 EAS AF: 0.141

Gnomad4 SAS AF: 0.163

Gnomad4 FIN AF: 0.137

Gnomad4 NFE AF: 0.161

Gnomad4 OTH AF: 0.149

Alfa AF: 0.137 Hom.: 161

Bravo AF: 0.128

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	7.4
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs708482; hg19: chr3-145180870;