rs2829946

Positions:

• chr21-25844046-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 0.15 in 152,160 control chromosomes in the GnomAD database, including 1,843 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 0.15 (1843 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.117

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.161 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.25844046C>T		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.150 AC: 22860 AN: 152042 Hom.: 1837 Cov.: 32

Gnomad AFR AF: 0.161

Gnomad AMI AF: 0.281

Gnomad AMR AF: 0.121

Gnomad ASJ AF: 0.0910

Gnomad EAS AF: 0.00309

Gnomad SAS AF: 0.0937

Gnomad FIN AF: 0.176

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.163

Gnomad OTH AF: 0.136

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

GnomAD4 genome AF: 0.150 AC: 22884 AN: 152160 Hom.: 1843 Cov.: 32 AF XY: 0.149 AC XY: 11094 AN XY: 74390

Gnomad4 AFR AF: 0.161

Gnomad4 AMR AF: 0.121

Gnomad4 ASJ AF: 0.0910

Gnomad4 EAS AF: 0.00329

Gnomad4 SAS AF: 0.0937

Gnomad4 FIN AF: 0.176

Gnomad4 NFE AF: 0.164

Gnomad4 OTH AF: 0.135

Alfa AF: 0.155 Hom.: 2956

Bravo AF: 0.147

Asia WGS AF: 0.0600 AC: 214 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	4.8
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2829946; hg19: chr21-27216357;