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. The variant received -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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.195 AC: 8091 AN: 41538

American (AMR) AF: 0.543 AC: 8300 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.544 AC: 1890 AN: 3472

East Asian (EAS) AF: 0.722 AC: 3708 AN: 5134

South Asian (SAS) AF: 0.768 AC: 3703 AN: 4822

European-Finnish (FIN) AF: 0.635 AC: 6719 AN: 10582

Middle Eastern (MID) AF: 0.609 AC: 179 AN: 294

European-Non Finnish (NFE) AF: 0.623 AC: 42327 AN: 67924

Other (OTH) AF: 0.554 AC: 1171 AN: 2112

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
PhyloP100		0.025

Splicing

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

Other links and lift over

dbSNP: rs879477; hg19: chr21-46399998;