20-22906619-C-T

Variant names:

• chr20-22906619-C-T
• rs6075982

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 0.256 in 151,968 control chromosomes in the GnomAD database, including 5,276 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 0.26 (5276 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.513
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.443 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: 0.256 AC: 38913 AN: 151852 Hom.: 5266 Cov.: 31

Gnomad AFR AF: 0.255

Gnomad AMI AF: 0.252

Gnomad AMR AF: 0.309

Gnomad ASJ AF: 0.196

Gnomad EAS AF: 0.458

Gnomad SAS AF: 0.368

Gnomad FIN AF: 0.266

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.224

Gnomad OTH AF: 0.257

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

GnomAD4 genome AF: 0.256 AC: 38954 AN: 151968 Hom.: 5276 Cov.: 31 AF XY: 0.262 AC XY: 19489 AN XY: 74252

African (AFR) AF: 0.254 AC: 10542 AN: 41436

American (AMR) AF: 0.310 AC: 4723 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.196 AC: 680 AN: 3470

East Asian (EAS) AF: 0.459 AC: 2363 AN: 5152

South Asian (SAS) AF: 0.367 AC: 1763 AN: 4800

European-Finnish (FIN) AF: 0.266 AC: 2813 AN: 10556

Middle Eastern (MID) AF: 0.264 AC: 77 AN: 292

European-Non Finnish (NFE) AF: 0.224 AC: 15216 AN: 67988

Other (OTH) AF: 0.260 AC: 548 AN: 2108

Alfa AF: 0.237 Hom.: 16730

Bravo AF: 0.257

Asia WGS AF: 0.402 AC: 1399 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	2.2
DANN	Benign	0.69
PhyloP100		-0.51

Splicing

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

Other links and lift over

dbSNP: rs6075982; hg19: chr20-22887257;