rs6445063

Positions:

• chr3-172475842-T-C

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 0.122 in 152,206 control chromosomes in the GnomAD database, including 1,215 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 0.12 (1215 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.66

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 (AFR) allele frequency at 95% confidence interval = 0.137 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: 0.122 AC: 18619 AN: 152090 Hom.: 1213 Cov.: 32

Gnomad AFR AF: 0.140

Gnomad AMI AF: 0.0647

Gnomad AMR AF: 0.116

Gnomad ASJ AF: 0.170

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.139

Gnomad FIN AF: 0.0632

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.129

Gnomad OTH AF: 0.126

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

GnomAD4 genome AF: 0.122 AC: 18638 AN: 152206 Hom.: 1215 Cov.: 32 AF XY: 0.121 AC XY: 8974 AN XY: 74400

Gnomad4 AFR AF: 0.140

Gnomad4 AMR AF: 0.116

Gnomad4 ASJ AF: 0.170

Gnomad4 EAS AF: 0.000386

Gnomad4 SAS AF: 0.138

Gnomad4 FIN AF: 0.0632

Gnomad4 NFE AF: 0.129

Gnomad4 OTH AF: 0.124

Alfa AF: 0.131 Hom.: 2804

Bravo AF: 0.127

Asia WGS AF: 0.0620 AC: 215 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	5.2
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6445063; hg19: chr3-172193632;