rs2012438

Positions:

• chr21-44983352-A-G

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 0.245 in 140,854 control chromosomes in the GnomAD database, including 4,891 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 0.24 (4891 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0640

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 (AFR) allele frequency at 95% confidence interval = 0.419 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.245 AC: 34436 AN: 140742 Hom.: 4891 Cov.: 34

Gnomad AFR AF: 0.425

Gnomad AMI AF: 0.204

Gnomad AMR AF: 0.275

Gnomad ASJ AF: 0.205

Gnomad EAS AF: 0.122

Gnomad SAS AF: 0.0732

Gnomad FIN AF: 0.180

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.162

Gnomad OTH AF: 0.219

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

GnomAD4 genome AF: 0.245 AC: 34460 AN: 140854 Hom.: 4891 Cov.: 34 AF XY: 0.244 AC XY: 16564 AN XY: 67838

Gnomad4 AFR AF: 0.425

Gnomad4 AMR AF: 0.275

Gnomad4 ASJ AF: 0.205

Gnomad4 EAS AF: 0.122

Gnomad4 SAS AF: 0.0718

Gnomad4 FIN AF: 0.180

Gnomad4 NFE AF: 0.162

Gnomad4 OTH AF: 0.219

Alfa AF: 0.192 Hom.: 774

Bravo AF: 0.244

Asia WGS AF: 0.106 AC: 368 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	2.0
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2012438; hg19: chr21-46403267;