rs6038393

Variant names:

• chr20-6249486-C-T
• rs6038393

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.536 AC: 22207 AN: 41396

American (AMR) AF: 0.269 AC: 4105 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.279 AC: 966 AN: 3468

East Asian (EAS) AF: 0.153 AC: 792 AN: 5178

South Asian (SAS) AF: 0.287 AC: 1381 AN: 4814

European-Finnish (FIN) AF: 0.252 AC: 2657 AN: 10552

Middle Eastern (MID) AF: 0.255 AC: 75 AN: 294

European-Non Finnish (NFE) AF: 0.222 AC: 15066 AN: 67976

Other (OTH) AF: 0.293 AC: 619 AN: 2112

Alfa AF: 0.267 Hom.: 2137

Bravo AF: 0.323

Asia WGS AF: 0.213 AC: 744 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	12
DANN	Benign	0.61
PhyloP100		0.10

Splicing

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

Other links and lift over

dbSNP: rs6038393; hg19: chr20-6230133;