rs6032064

Variant names:

• chr20-45226186-A-G
• rs6032064

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 0.162 in 152,112 control chromosomes in the GnomAD database, including 2,071 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 0.16 (2071 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.19

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.176 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: 0.161 AC: 24532 AN: 151994 Hom.: 2061 Cov.: 32

Gnomad AFR AF: 0.148

Gnomad AMI AF: 0.316

Gnomad AMR AF: 0.135

Gnomad ASJ AF: 0.164

Gnomad EAS AF: 0.0366

Gnomad SAS AF: 0.146

Gnomad FIN AF: 0.191

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.179

Gnomad OTH AF: 0.169

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

GnomAD4 genome AF: 0.162 AC: 24583 AN: 152112 Hom.: 2071 Cov.: 32 AF XY: 0.162 AC XY: 12027 AN XY: 74340

Gnomad4 AFR AF: 0.149

Gnomad4 AMR AF: 0.135

Gnomad4 ASJ AF: 0.164

Gnomad4 EAS AF: 0.0365

Gnomad4 SAS AF: 0.148

Gnomad4 FIN AF: 0.191

Gnomad4 NFE AF: 0.179

Gnomad4 OTH AF: 0.173

Alfa AF: 0.158 Hom.: 505

Bravo AF: 0.156

Asia WGS AF: 0.0940 AC: 327 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.093
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6032064; hg19: chr20-43854827;