rs6032664

chr20-46110780-A-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 0.793 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;