20-21994388-T-C

Variant names:

• chr20-21994388-T-C
• rs6106438

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 0.531 in 151,834 control chromosomes in the GnomAD database, including 22,393 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 0.53 (22393 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0600
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.678 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: 0.530 AC: 80474 AN: 151714 Hom.: 22336 Cov.: 30

Gnomad AFR AF: 0.684

Gnomad AMI AF: 0.489

Gnomad AMR AF: 0.628

Gnomad ASJ AF: 0.472

Gnomad EAS AF: 0.505

Gnomad SAS AF: 0.509

Gnomad FIN AF: 0.376

Gnomad MID AF: 0.573

Gnomad NFE AF: 0.446

Gnomad OTH AF: 0.540

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

GnomAD4 genome AF: 0.531 AC: 80591 AN: 151834 Hom.: 22393 Cov.: 30 AF XY: 0.528 AC XY: 39184 AN XY: 74206

African (AFR) AF: 0.684 AC: 28344 AN: 41426

American (AMR) AF: 0.628 AC: 9582 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.472 AC: 1638 AN: 3470

East Asian (EAS) AF: 0.505 AC: 2577 AN: 5102

South Asian (SAS) AF: 0.508 AC: 2430 AN: 4780

European-Finnish (FIN) AF: 0.376 AC: 3968 AN: 10548

Middle Eastern (MID) AF: 0.554 AC: 163 AN: 294

European-Non Finnish (NFE) AF: 0.446 AC: 30293 AN: 67944

Other (OTH) AF: 0.546 AC: 1152 AN: 2110

Alfa AF: 0.545 Hom.: 5341

Bravo AF: 0.558

Asia WGS AF: 0.579 AC: 2013 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.1
DANN	Benign	0.51
PhyloP100		0.060

Splicing

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

Other links and lift over

dbSNP: rs6106438; hg19: chr20-21975026;