rs1998149

Variant names:

• chr20-33234364-C-A
• rs1998149

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 0.266 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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.364 AC: 15089 AN: 41486

American (AMR) AF: 0.149 AC: 2284 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.146 AC: 506 AN: 3468

East Asian (EAS) AF: 0.213 AC: 1098 AN: 5164

South Asian (SAS) AF: 0.204 AC: 981 AN: 4820

European-Finnish (FIN) AF: 0.263 AC: 2785 AN: 10594

Middle Eastern (MID) AF: 0.224 AC: 66 AN: 294

European-Non Finnish (NFE) AF: 0.249 AC: 16937 AN: 67970

Other (OTH) AF: 0.236 AC: 500 AN: 2116

Alfa AF: 0.267 Hom.: 750

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
PhyloP100		-0.94

Splicing

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

Other links and lift over

dbSNP: rs1998149; hg19: chr20-31822170;