rs879477

Variant names:

• chr21-44980083-G-A
• rs879477

Your query was ambiguous. Multiple possible variants found:

• chr21-44980083-G-A
• chr21-44980083-G-C
• chr21-44980083-G-T

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;