rs517871

Variant names:

• chr21-39537779-G-A
• rs517871

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 0.584 in 151,566 control chromosomes in the GnomAD database, including 27,561 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 0.58 (27561 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.629

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.668 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: 0.584 AC: 88472 AN: 151448 Hom.: 27557 Cov.: 32

Gnomad AFR AF: 0.353

Gnomad AMI AF: 0.623

Gnomad AMR AF: 0.678

Gnomad ASJ AF: 0.628

Gnomad EAS AF: 0.560

Gnomad SAS AF: 0.648

Gnomad FIN AF: 0.804

Gnomad MID AF: 0.580

Gnomad NFE AF: 0.664

Gnomad OTH AF: 0.600

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

GnomAD4 genome AF: 0.584 AC: 88495 AN: 151566 Hom.: 27561 Cov.: 32 AF XY: 0.592 AC XY: 43833 AN XY: 74038

Gnomad4 AFR AF: 0.353

Gnomad4 AMR AF: 0.678

Gnomad4 ASJ AF: 0.628

Gnomad4 EAS AF: 0.559

Gnomad4 SAS AF: 0.648

Gnomad4 FIN AF: 0.804

Gnomad4 NFE AF: 0.664

Gnomad4 OTH AF: 0.600

Alfa AF: 0.650 Hom.: 65546

Bravo AF: 0.561

Asia WGS AF: 0.624 AC: 2170 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	0.83
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs517871; hg19: chr21-40909706;