chr20-6382833-C-T

Position:

• chr20-6382833-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 0.234 in 151,512 control chromosomes in the GnomAD database, including 4,848 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 0.23 (4848 hom., cov: 30)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00300

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.3 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.6382833C>T		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.234 AC: 35405 AN: 151390 Hom.: 4851 Cov.: 30

Gnomad AFR AF: 0.0848

Gnomad AMI AF: 0.308

Gnomad AMR AF: 0.259

Gnomad ASJ AF: 0.413

Gnomad EAS AF: 0.204

Gnomad SAS AF: 0.307

Gnomad FIN AF: 0.240

Gnomad MID AF: 0.364

Gnomad NFE AF: 0.303

Gnomad OTH AF: 0.265

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

GnomAD4 genome AF: 0.234 AC: 35401 AN: 151512 Hom.: 4848 Cov.: 30 AF XY: 0.231 AC XY: 17090 AN XY: 73980

Gnomad4 AFR AF: 0.0846

Gnomad4 AMR AF: 0.259

Gnomad4 ASJ AF: 0.413

Gnomad4 EAS AF: 0.204

Gnomad4 SAS AF: 0.307

Gnomad4 FIN AF: 0.240

Gnomad4 NFE AF: 0.303

Gnomad4 OTH AF: 0.264

Alfa AF: 0.304 Hom.: 10542

Bravo AF: 0.226

Asia WGS AF: 0.240 AC: 837 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.8
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: rs2148815; hg19: chr20-6363480;