20-46110780-A-T

Variant names:

• chr20-46110780-A-T
• rs6032664

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 0.793 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
• Publications: 24 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.939 AC: 39028 AN: 41544

American (AMR) AF: 0.776 AC: 11856 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.731 AC: 2534 AN: 3468

East Asian (EAS) AF: 0.573 AC: 2962 AN: 5170

South Asian (SAS) AF: 0.738 AC: 3556 AN: 4820

European-Finnish (FIN) AF: 0.722 AC: 7616 AN: 10552

Middle Eastern (MID) AF: 0.721 AC: 212 AN: 294

European-Non Finnish (NFE) AF: 0.743 AC: 50523 AN: 67994

Other (OTH) AF: 0.766 AC: 1620 AN: 2114

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.4
DANN	Benign	0.83
PhyloP100		-0.16

Splicing

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

Other links and lift over

dbSNP: rs6032664; hg19: chr20-44739419;