rs3788266

Positions:

• chr21-46606442-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 0.496 in 152,206 control chromosomes in the GnomAD database, including 19,008 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 (19008 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.937

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 (AFR) allele frequency at 95% confidence interval = 0.536 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: 0.496 AC: 75496 AN: 152088 Hom.: 18993 Cov.: 34

Gnomad AFR AF: 0.542

Gnomad AMI AF: 0.535

Gnomad AMR AF: 0.488

Gnomad ASJ AF: 0.498

Gnomad EAS AF: 0.260

Gnomad SAS AF: 0.372

Gnomad FIN AF: 0.573

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.485

Gnomad OTH AF: 0.509

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

GnomAD4 genome AF: 0.496 AC: 75561 AN: 152206 Hom.: 19008 Cov.: 34 AF XY: 0.500 AC XY: 37227 AN XY: 74412

Gnomad4 AFR AF: 0.542

Gnomad4 AMR AF: 0.488

Gnomad4 ASJ AF: 0.498

Gnomad4 EAS AF: 0.260

Gnomad4 SAS AF: 0.373

Gnomad4 FIN AF: 0.573

Gnomad4 NFE AF: 0.485

Gnomad4 OTH AF: 0.504

Alfa AF: 0.491 Hom.: 7517

Bravo AF: 0.492

Asia WGS AF: 0.325 AC: 1131 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	0.19
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3788266; hg19: chr21-48026355;