chr3-145463083-C-T

Position:

• chr3-145463083-C-T

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;