rs6445063

Variant names:

• chr3-172475842-T-C
• rs6445063

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 9 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.140 AC: 5808 AN: 41512

American (AMR) AF: 0.116 AC: 1778 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.170 AC: 591 AN: 3470

East Asian (EAS) AF: 0.000386 AC: 2 AN: 5188

South Asian (SAS) AF: 0.138 AC: 665 AN: 4816

European-Finnish (FIN) AF: 0.0632 AC: 670 AN: 10594

Middle Eastern (MID) AF: 0.173 AC: 51 AN: 294

European-Non Finnish (NFE) AF: 0.129 AC: 8752 AN: 68008

Other (OTH) AF: 0.124 AC: 262 AN: 2114

Alfa AF: 0.130 Hom.: 4390

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
PhyloP100		1.7

Splicing

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

Other links and lift over

dbSNP: rs6445063; hg19: chr3-172193632;