rs1998149

chr20-33234364-C-A

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 0.266 in 152,120 control chromosomes in the GnomAD database, including 5,894 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 0.27 (5894 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.944

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.359 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: 0.266 AC: 40430 AN: 152002 Hom.: 5875 Cov.: 32

Gnomad AFR AF: 0.363

Gnomad AMI AF: 0.279

Gnomad AMR AF: 0.150

Gnomad ASJ AF: 0.146

Gnomad EAS AF: 0.212

Gnomad SAS AF: 0.203

Gnomad FIN AF: 0.263

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.249

Gnomad OTH AF: 0.232

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

GnomAD4 genome AF: 0.266 AC: 40500 AN: 152120 Hom.: 5894 Cov.: 32 AF XY: 0.264 AC XY: 19625 AN XY: 74382

Gnomad4 AFR AF: 0.364

Gnomad4 AMR AF: 0.149

Gnomad4 ASJ AF: 0.146

Gnomad4 EAS AF: 0.213

Gnomad4 SAS AF: 0.204

Gnomad4 FIN AF: 0.263

Gnomad4 NFE AF: 0.249

Gnomad4 OTH AF: 0.236

Alfa AF: 0.263 Hom.: 691

Bravo AF: 0.262

Asia WGS AF: 0.245 AC: 850 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	1.2
Dann	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1998149; hg19: chr20-31822170;