rs2012438

Variant names:

• chr21-44983352-A-G
• rs2012438

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;