rs6517581

Positions:

• chr21-39982941-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 0.534 in 152,082 control chromosomes in the GnomAD database, including 22,347 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 0.53 (22347 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.489

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 (NFE) allele frequency at 95% confidence interval = 0.579 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: 0.535 AC: 81242 AN: 151962 Hom.: 22329 Cov.: 33

Gnomad AFR AF: 0.530

Gnomad AMI AF: 0.386

Gnomad AMR AF: 0.437

Gnomad ASJ AF: 0.646

Gnomad EAS AF: 0.235

Gnomad SAS AF: 0.468

Gnomad FIN AF: 0.524

Gnomad MID AF: 0.545

Gnomad NFE AF: 0.584

Gnomad OTH AF: 0.565

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

GnomAD4 genome AF: 0.534 AC: 81281 AN: 152082 Hom.: 22347 Cov.: 33 AF XY: 0.527 AC XY: 39177 AN XY: 74326

Gnomad4 AFR AF: 0.530

Gnomad4 AMR AF: 0.437

Gnomad4 ASJ AF: 0.646

Gnomad4 EAS AF: 0.235

Gnomad4 SAS AF: 0.469

Gnomad4 FIN AF: 0.524

Gnomad4 NFE AF: 0.583

Gnomad4 OTH AF: 0.563

Alfa AF: 0.572 Hom.: 52072

Bravo AF: 0.524

Asia WGS AF: 0.393 AC: 1373 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	0.82
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6517581; hg19: chr21-41354868;