21-39972984-T-G

Variant names:

• chr21-39972984-T-G
• rs1734920

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 0.664 in 152,056 control chromosomes in the GnomAD database, including 34,177 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 0.66 (34177 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.605

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.791 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: 0.664 AC: 100949 AN: 151936 Hom.: 34136 Cov.: 32

Gnomad AFR AF: 0.799

Gnomad AMI AF: 0.413

Gnomad AMR AF: 0.635

Gnomad ASJ AF: 0.660

Gnomad EAS AF: 0.672

Gnomad SAS AF: 0.687

Gnomad FIN AF: 0.654

Gnomad MID AF: 0.640

Gnomad NFE AF: 0.593

Gnomad OTH AF: 0.648

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

GnomAD4 genome AF: 0.664 AC: 101038 AN: 152056 Hom.: 34177 Cov.: 32 AF XY: 0.669 AC XY: 49686 AN XY: 74316

Gnomad4 AFR AF: 0.798

Gnomad4 AMR AF: 0.635

Gnomad4 ASJ AF: 0.660

Gnomad4 EAS AF: 0.672

Gnomad4 SAS AF: 0.687

Gnomad4 FIN AF: 0.654

Gnomad4 NFE AF: 0.593

Gnomad4 OTH AF: 0.652

Alfa AF: 0.603 Hom.: 29926

Bravo AF: 0.670

Asia WGS AF: 0.700 AC: 2435 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.28
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1734920; hg19: chr21-41344911;