chr20-22234183-C-T

Variant names:

• chr20-22234183-C-T
• rs1337906

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 0.336 in 152,168 control chromosomes in the GnomAD database, including 9,178 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 0.34 (9178 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.27
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.63).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.665 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: 0.336 AC: 51150 AN: 152050 Hom.: 9176 Cov.: 33

Gnomad AFR AF: 0.246

Gnomad AMI AF: 0.276

Gnomad AMR AF: 0.396

Gnomad ASJ AF: 0.414

Gnomad EAS AF: 0.684

Gnomad SAS AF: 0.373

Gnomad FIN AF: 0.274

Gnomad MID AF: 0.402

Gnomad NFE AF: 0.354

Gnomad OTH AF: 0.373

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

GnomAD4 genome AF: 0.336 AC: 51172 AN: 152168 Hom.: 9178 Cov.: 33 AF XY: 0.336 AC XY: 24978 AN XY: 74402

African (AFR) AF: 0.245 AC: 10188 AN: 41522

American (AMR) AF: 0.396 AC: 6051 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.414 AC: 1437 AN: 3470

East Asian (EAS) AF: 0.684 AC: 3542 AN: 5178

South Asian (SAS) AF: 0.373 AC: 1796 AN: 4818

European-Finnish (FIN) AF: 0.274 AC: 2894 AN: 10572

Middle Eastern (MID) AF: 0.405 AC: 119 AN: 294

European-Non Finnish (NFE) AF: 0.354 AC: 24103 AN: 68008

Other (OTH) AF: 0.375 AC: 791 AN: 2110

Alfa AF: 0.353 Hom.: 8266

Bravo AF: 0.343

Asia WGS AF: 0.476 AC: 1655 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.63
CADD	Benign	10
DANN	Benign	0.65
PhyloP100		1.3

Splicing

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

Other links and lift over

dbSNP: rs1337906; hg19: chr20-22214821;