21-44985839-G-A

Position:

• chr21-44985839-G-A

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 0.803 in 152,176 control chromosomes in the GnomAD database, including 49,155 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 0.80 (49155 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.70

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.829 is higher than 0.05.

Transcripts

RefSeq

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

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.803 AC: 122091 AN: 152058 Hom.: 49115 Cov.: 33

Gnomad AFR AF: 0.836

Gnomad AMI AF: 0.750

Gnomad AMR AF: 0.816

Gnomad ASJ AF: 0.775

Gnomad EAS AF: 0.831

Gnomad SAS AF: 0.824

Gnomad FIN AF: 0.790

Gnomad MID AF: 0.775

Gnomad NFE AF: 0.781

Gnomad OTH AF: 0.801

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

GnomAD4 genome AF: 0.803 AC: 122190 AN: 152176 Hom.: 49155 Cov.: 33 AF XY: 0.802 AC XY: 59672 AN XY: 74396

Gnomad4 AFR AF: 0.836

Gnomad4 AMR AF: 0.816

Gnomad4 ASJ AF: 0.775

Gnomad4 EAS AF: 0.830

Gnomad4 SAS AF: 0.824

Gnomad4 FIN AF: 0.790

Gnomad4 NFE AF: 0.781

Gnomad4 OTH AF: 0.802

Alfa AF: 0.795 Hom.: 13689

Bravo AF: 0.803

Asia WGS AF: 0.841 AC: 2922 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.40
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs914207; hg19: chr21-46405754;