rs1124933

Variant names:

• chr20-18097908-G-A
• rs1124933

Your query was ambiguous. Multiple possible variants found:

• chr20-18097908-G-A
• chr20-18097908-G-C
• chr20-18097908-G-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 0.437 in 151,744 control chromosomes in the GnomAD database, including 15,413 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 0.44 (15413 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.115

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.886 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: 0.437 AC: 66291 AN: 151626 Hom.: 15401 Cov.: 31

Gnomad AFR AF: 0.362

Gnomad AMI AF: 0.419

Gnomad AMR AF: 0.527

Gnomad ASJ AF: 0.369

Gnomad EAS AF: 0.907

Gnomad SAS AF: 0.631

Gnomad FIN AF: 0.422

Gnomad MID AF: 0.364

Gnomad NFE AF: 0.420

Gnomad OTH AF: 0.434

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

GnomAD4 genome AF: 0.437 AC: 66340 AN: 151744 Hom.: 15413 Cov.: 31 AF XY: 0.446 AC XY: 33033 AN XY: 74138

Gnomad4 AFR AF: 0.362

Gnomad4 AMR AF: 0.528

Gnomad4 ASJ AF: 0.369

Gnomad4 EAS AF: 0.908

Gnomad4 SAS AF: 0.631

Gnomad4 FIN AF: 0.422

Gnomad4 NFE AF: 0.420

Gnomad4 OTH AF: 0.440

Alfa AF: 0.430 Hom.: 19732

Bravo AF: 0.443

Asia WGS AF: 0.753 AC: 2618 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.0
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1124933; hg19: chr20-18078552;