20-6257494-G-A

Position:

• chr20-6257494-G-A

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.316 in 152,100 control chromosomes in the GnomAD database, including 9,139 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 0.32 (9139 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.48

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.37).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.531 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: 0.316 AC: 47974 AN: 151982 Hom.: 9116 Cov.: 32

Gnomad AFR AF: 0.537

Gnomad AMI AF: 0.120

Gnomad AMR AF: 0.268

Gnomad ASJ AF: 0.281

Gnomad EAS AF: 0.153

Gnomad SAS AF: 0.285

Gnomad FIN AF: 0.251

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.222

Gnomad OTH AF: 0.295

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

GnomAD4 genome AF: 0.316 AC: 48035 AN: 152100 Hom.: 9139 Cov.: 32 AF XY: 0.315 AC XY: 23428 AN XY: 74342

Gnomad4 AFR AF: 0.537

Gnomad4 AMR AF: 0.268

Gnomad4 ASJ AF: 0.281

Gnomad4 EAS AF: 0.153

Gnomad4 SAS AF: 0.287

Gnomad4 FIN AF: 0.251

Gnomad4 NFE AF: 0.222

Gnomad4 OTH AF: 0.293

Alfa AF: 0.250 Hom.: 4684

Bravo AF: 0.323

Asia WGS AF: 0.214 AC: 747 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.37
CADD	Benign	14
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6038397; hg19: chr20-6238141;