chr20-6394813-T-A

Position:

• chr20-6394813-T-A

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 0.294 in 152,080 control chromosomes in the GnomAD database, including 6,769 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 0.29 (6769 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.702

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.32 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.294 AC: 44736 AN: 151962 Hom.: 6770 Cov.: 32

Gnomad AFR AF: 0.325

Gnomad AMI AF: 0.223

Gnomad AMR AF: 0.263

Gnomad ASJ AF: 0.360

Gnomad EAS AF: 0.110

Gnomad SAS AF: 0.247

Gnomad FIN AF: 0.248

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.304

Gnomad OTH AF: 0.320

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

GnomAD4 genome AF: 0.294 AC: 44742 AN: 152080 Hom.: 6769 Cov.: 32 AF XY: 0.288 AC XY: 21369 AN XY: 74320

Gnomad4 AFR AF: 0.324

Gnomad4 AMR AF: 0.263

Gnomad4 ASJ AF: 0.360

Gnomad4 EAS AF: 0.110

Gnomad4 SAS AF: 0.248

Gnomad4 FIN AF: 0.248

Gnomad4 NFE AF: 0.304

Gnomad4 OTH AF: 0.317

Alfa AF: 0.297 Hom.: 795

Bravo AF: 0.294

Asia WGS AF: 0.206 AC: 714 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	12
DANN	Benign	0.85

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6085533; hg19: chr20-6375460;