rs1337906

Positions:

• chr20-22234183-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 0.336 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.245

Gnomad4 AMR AF: 0.396

Gnomad4 ASJ AF: 0.414

Gnomad4 EAS AF: 0.684

Gnomad4 SAS AF: 0.373

Gnomad4 FIN AF: 0.274

Gnomad4 NFE AF: 0.354

Gnomad4 OTH AF: 0.375

Alfa AF: 0.354 Hom.: 7054

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1337906; hg19: chr20-22214821;