rs2329945

Positions:

• chr21-44989099-C-A
• chr21-44989099-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 0.181 in 152,188 control chromosomes in the GnomAD database, including 2,641 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 0.18 (2641 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.94

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.238 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: 0.181 AC: 27480 AN: 152070 Hom.: 2643 Cov.: 33

Gnomad AFR AF: 0.134

Gnomad AMI AF: 0.203

Gnomad AMR AF: 0.244

Gnomad ASJ AF: 0.239

Gnomad EAS AF: 0.170

Gnomad SAS AF: 0.120

Gnomad FIN AF: 0.180

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.197

Gnomad OTH AF: 0.174

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

GnomAD4 genome AF: 0.181 AC: 27485 AN: 152188 Hom.: 2641 Cov.: 33 AF XY: 0.181 AC XY: 13496 AN XY: 74418

Gnomad4 AFR AF: 0.134

Gnomad4 AMR AF: 0.244

Gnomad4 ASJ AF: 0.239

Gnomad4 EAS AF: 0.170

Gnomad4 SAS AF: 0.120

Gnomad4 FIN AF: 0.180

Gnomad4 NFE AF: 0.197

Gnomad4 OTH AF: 0.177

Alfa AF: 0.103 Hom.: 157

Bravo AF: 0.186

Asia WGS AF: 0.158 AC: 550 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.5
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2329945; hg19: chr21-46409014;