20-6382833-C-T

Variant names:

• chr20-6382833-C-T
• rs2148815

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 0.234 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: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00300
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.0846 AC: 3495 AN: 41306

American (AMR) AF: 0.259 AC: 3931 AN: 15206

Ashkenazi Jewish (ASJ) AF: 0.413 AC: 1431 AN: 3464

East Asian (EAS) AF: 0.204 AC: 1038 AN: 5090

South Asian (SAS) AF: 0.307 AC: 1467 AN: 4784

European-Finnish (FIN) AF: 0.240 AC: 2513 AN: 10478

Middle Eastern (MID) AF: 0.357 AC: 105 AN: 294

European-Non Finnish (NFE) AF: 0.303 AC: 20583 AN: 67872

Other (OTH) AF: 0.264 AC: 557 AN: 2106

Alfa AF: 0.296 Hom.: 13918

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
PhyloP100		-0.0030

Splicing

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

Other links and lift over

dbSNP: rs2148815; hg19: chr20-6363480;