rs1984023

Variant names:

• chr21-39820276-G-A
• rs1984023

Your query was ambiguous. Multiple possible variants found:

• chr21-39820276-G-A
• chr21-39820276-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 0.351 in 151,928 control chromosomes in the GnomAD database, including 9,721 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 0.35 (9721 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.754

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.454 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: 0.350 AC: 53185 AN: 151810 Hom.: 9691 Cov.: 32

Gnomad AFR AF: 0.382

Gnomad AMI AF: 0.370

Gnomad AMR AF: 0.455

Gnomad ASJ AF: 0.379

Gnomad EAS AF: 0.468

Gnomad SAS AF: 0.360

Gnomad FIN AF: 0.301

Gnomad MID AF: 0.315

Gnomad NFE AF: 0.305

Gnomad OTH AF: 0.336

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

GnomAD4 genome AF: 0.351 AC: 53264 AN: 151928 Hom.: 9721 Cov.: 32 AF XY: 0.354 AC XY: 26302 AN XY: 74216

Gnomad4 AFR AF: 0.382

Gnomad4 AMR AF: 0.456

Gnomad4 ASJ AF: 0.379

Gnomad4 EAS AF: 0.469

Gnomad4 SAS AF: 0.362

Gnomad4 FIN AF: 0.301

Gnomad4 NFE AF: 0.305

Gnomad4 OTH AF: 0.339

Alfa AF: 0.313 Hom.: 10382

Bravo AF: 0.366

Asia WGS AF: 0.404 AC: 1406 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.10
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1984023; hg19: chr21-41192203;