20-6407421-T-C

Variant names:

• chr20-6407421-T-C
• rs355527

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 0.738 in 151,842 control chromosomes in the GnomAD database, including 41,798 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 0.74 (41798 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.908
• Publications: 21 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.885 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.738 AC: 111965 AN: 151724 Hom.: 41746 Cov.: 30

Gnomad AFR AF: 0.826

Gnomad AMI AF: 0.567

Gnomad AMR AF: 0.748

Gnomad ASJ AF: 0.732

Gnomad EAS AF: 0.907

Gnomad SAS AF: 0.702

Gnomad FIN AF: 0.720

Gnomad MID AF: 0.788

Gnomad NFE AF: 0.677

Gnomad OTH AF: 0.751

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

GnomAD4 genome AF: 0.738 AC: 112076 AN: 151842 Hom.: 41798 Cov.: 30 AF XY: 0.739 AC XY: 54805 AN XY: 74148

African (AFR) AF: 0.826 AC: 34181 AN: 41388

American (AMR) AF: 0.749 AC: 11427 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.732 AC: 2539 AN: 3470

East Asian (EAS) AF: 0.906 AC: 4672 AN: 5154

South Asian (SAS) AF: 0.703 AC: 3374 AN: 4800

European-Finnish (FIN) AF: 0.720 AC: 7556 AN: 10494

Middle Eastern (MID) AF: 0.779 AC: 229 AN: 294

European-Non Finnish (NFE) AF: 0.677 AC: 45998 AN: 67962

Other (OTH) AF: 0.752 AC: 1583 AN: 2104

Alfa AF: 0.707 Hom.: 21572

Bravo AF: 0.749

Asia WGS AF: 0.780 AC: 2715 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.59
DANN	Benign	0.63
PhyloP100		-0.91

Splicing

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

Other links and lift over

dbSNP: rs355527; hg19: chr20-6388068;