21-44980083-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 0.504 in 152,062 control chromosomes in the GnomAD database, including 22,287 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 0.50 (22287 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0250

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.747 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: 0.504 AC: 76581 AN: 151944 Hom.: 22287 Cov.: 33

Gnomad AFR AF: 0.195

Gnomad AMI AF: 0.562

Gnomad AMR AF: 0.543

Gnomad ASJ AF: 0.544

Gnomad EAS AF: 0.723

Gnomad SAS AF: 0.766

Gnomad FIN AF: 0.635

Gnomad MID AF: 0.608

Gnomad NFE AF: 0.623

Gnomad OTH AF: 0.551

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

GnomAD4 genome AF: 0.504 AC: 76598 AN: 152062 Hom.: 22287 Cov.: 33 AF XY: 0.509 AC XY: 37854 AN XY: 74318

Gnomad4 AFR AF: 0.195

Gnomad4 AMR AF: 0.543

Gnomad4 ASJ AF: 0.544

Gnomad4 EAS AF: 0.722

Gnomad4 SAS AF: 0.768

Gnomad4 FIN AF: 0.635

Gnomad4 NFE AF: 0.623

Gnomad4 OTH AF: 0.554

Alfa AF: 0.449 Hom.: 1575

Bravo AF: 0.478

Asia WGS AF: 0.709 AC: 2462 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	2.5
Dann	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs879477; hg19: chr21-46399998;