rs6038397

Variant names:

• chr20-6257494-G-A
• rs6038397

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;