chr20-6407421-T-C

Variant names:

• chr20-6407421-T-C
• rs355527

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 0.738 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.738 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

Gnomad4 AFR AF: 0.826

Gnomad4 AMR AF: 0.749

Gnomad4 ASJ AF: 0.732

Gnomad4 EAS AF: 0.906

Gnomad4 SAS AF: 0.703

Gnomad4 FIN AF: 0.720

Gnomad4 NFE AF: 0.677

Gnomad4 OTH AF: 0.752

Alfa AF: 0.713 Hom.: 12887

Bravo AF: 0.749

Asia WGS AF: 0.780 AC: 2715 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs355527; hg19: chr20-6388068;