rs2032314

Positions:

• chr21-33982222-T-C
• chr21-33982222-T-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 0.863 in 152,070 control chromosomes in the GnomAD database, including 57,180 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 0.86 (57180 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.992

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.925 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.863 AC: 131108 AN: 151952 Hom.: 57153 Cov.: 30

Gnomad AFR AF: 0.733

Gnomad AMI AF: 0.878

Gnomad AMR AF: 0.877

Gnomad ASJ AF: 0.869

Gnomad EAS AF: 0.754

Gnomad SAS AF: 0.889

Gnomad FIN AF: 0.947

Gnomad MID AF: 0.858

Gnomad NFE AF: 0.931

Gnomad OTH AF: 0.873

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

GnomAD4 genome AF: 0.863 AC: 131187 AN: 152070 Hom.: 57180 Cov.: 30 AF XY: 0.864 AC XY: 64244 AN XY: 74342

Gnomad4 AFR AF: 0.733

Gnomad4 AMR AF: 0.877

Gnomad4 ASJ AF: 0.869

Gnomad4 EAS AF: 0.753

Gnomad4 SAS AF: 0.888

Gnomad4 FIN AF: 0.947

Gnomad4 NFE AF: 0.931

Gnomad4 OTH AF: 0.874

Alfa AF: 0.913 Hom.: 126531

Bravo AF: 0.849

Asia WGS AF: 0.847 AC: 2948 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.53
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2032314; hg19: chr21-35354523;