rs2012438

Variant names:

• chr21-44983352-A-G
• rs2012438

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.425 AC: 16454 AN: 38736

American (AMR) AF: 0.275 AC: 3734 AN: 13578

Ashkenazi Jewish (ASJ) AF: 0.205 AC: 688 AN: 3348

East Asian (EAS) AF: 0.122 AC: 570 AN: 4678

South Asian (SAS) AF: 0.0718 AC: 273 AN: 3804

European-Finnish (FIN) AF: 0.180 AC: 1630 AN: 9050

Middle Eastern (MID) AF: 0.118 AC: 33 AN: 280

European-Non Finnish (NFE) AF: 0.162 AC: 10489 AN: 64628

Other (OTH) AF: 0.219 AC: 416 AN: 1902

Alfa AF: 0.197 Hom.: 830

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
PhyloP100		-0.064

Splicing

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

Other links and lift over

dbSNP: rs2012438; hg19: chr21-46403267;