rs6032664

Variant names:

• chr20-46110780-A-T
• rs6032664

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 0.793 in 152,148 control chromosomes in the GnomAD database, including 48,547 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 0.79 (48547 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.164

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.932 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: 0.792 AC: 120463 AN: 152030 Hom.: 48473 Cov.: 32

Gnomad AFR AF: 0.939

Gnomad AMI AF: 0.759

Gnomad AMR AF: 0.775

Gnomad ASJ AF: 0.731

Gnomad EAS AF: 0.572

Gnomad SAS AF: 0.738

Gnomad FIN AF: 0.722

Gnomad MID AF: 0.722

Gnomad NFE AF: 0.743

Gnomad OTH AF: 0.763

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

GnomAD4 genome AF: 0.793 AC: 120598 AN: 152148 Hom.: 48547 Cov.: 32 AF XY: 0.787 AC XY: 58542 AN XY: 74360

Gnomad4 AFR AF: 0.939

Gnomad4 AMR AF: 0.776

Gnomad4 ASJ AF: 0.731

Gnomad4 EAS AF: 0.573

Gnomad4 SAS AF: 0.738

Gnomad4 FIN AF: 0.722

Gnomad4 NFE AF: 0.743

Gnomad4 OTH AF: 0.766

Alfa AF: 0.781 Hom.: 5819

Bravo AF: 0.803

Asia WGS AF: 0.725 AC: 2522 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.4
DANN	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6032664; hg19: chr20-44739419;