21-44983382-G-C

Variant names:

• chr21-44983382-G-C
• rs12626362

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 0.399 in 25,134 control chromosomes in the GnomAD database, including 604 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 0.40 (604 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.308

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.552 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: 0.399 AC: 10013 AN: 25114 Hom.: 604 Cov.: 32

Gnomad AFR AF: 0.271

Gnomad AMI AF: 0.437

Gnomad AMR AF: 0.478

Gnomad ASJ AF: 0.384

Gnomad EAS AF: 0.576

Gnomad SAS AF: 0.513

Gnomad FIN AF: 0.432

Gnomad MID AF: 0.414

Gnomad NFE AF: 0.334

Gnomad OTH AF: 0.428

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

GnomAD4 genome AF: 0.399 AC: 10017 AN: 25134 Hom.: 604 Cov.: 32 AF XY: 0.413 AC XY: 5217 AN XY: 12640

Gnomad4 AFR AF: 0.270

Gnomad4 AMR AF: 0.479

Gnomad4 ASJ AF: 0.384

Gnomad4 EAS AF: 0.575

Gnomad4 SAS AF: 0.513

Gnomad4 FIN AF: 0.432

Gnomad4 NFE AF: 0.334

Gnomad4 OTH AF: 0.424

Alfa AF: 0.00872 Hom.: 3

Bravo AF: 0.0669

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	4.5
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12626362; hg19: chr21-46403297;