rs6038393

chr20-6249486-C-T

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 0.316 in 151,974 control chromosomes in the GnomAD database, including 9,113 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 (9113 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.103

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• 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	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.316 AC: 47919 AN: 151856 Hom.: 9093 Cov.: 32

Gnomad AFR AF: 0.536

Gnomad AMI AF: 0.120

Gnomad AMR AF: 0.269

Gnomad ASJ AF: 0.279

Gnomad EAS AF: 0.153

Gnomad SAS AF: 0.286

Gnomad FIN AF: 0.252

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.222

Gnomad OTH AF: 0.296

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

GnomAD4 genome AF: 0.316 AC: 47977 AN: 151974 Hom.: 9113 Cov.: 32 AF XY: 0.315 AC XY: 23409 AN XY: 74290

Gnomad4 AFR AF: 0.536

Gnomad4 AMR AF: 0.269

Gnomad4 ASJ AF: 0.279

Gnomad4 EAS AF: 0.153

Gnomad4 SAS AF: 0.287

Gnomad4 FIN AF: 0.252

Gnomad4 NFE AF: 0.222

Gnomad4 OTH AF: 0.293

Alfa AF: 0.262 Hom.: 1022

Bravo AF: 0.323

Asia WGS AF: 0.213 AC: 744 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	12
Dann	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6038393; hg19: chr20-6230133;