21-44759683-C-T

Variant names:

• chr21-44759683-C-T
• rs674696

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 0.432 in 152,220 control chromosomes in the GnomAD database, including 15,716 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 0.43 (15716 hom., cov: 35)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.24

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.691 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: 0.432 AC: 65747 AN: 152102 Hom.: 15698 Cov.: 35

Gnomad AFR AF: 0.612

Gnomad AMI AF: 0.238

Gnomad AMR AF: 0.449

Gnomad ASJ AF: 0.374

Gnomad EAS AF: 0.710

Gnomad SAS AF: 0.454

Gnomad FIN AF: 0.409

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.307

Gnomad OTH AF: 0.411

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

GnomAD4 genome AF: 0.432 AC: 65815 AN: 152220 Hom.: 15716 Cov.: 35 AF XY: 0.438 AC XY: 32585 AN XY: 74412

Gnomad4 AFR AF: 0.611

Gnomad4 AMR AF: 0.449

Gnomad4 ASJ AF: 0.374

Gnomad4 EAS AF: 0.710

Gnomad4 SAS AF: 0.454

Gnomad4 FIN AF: 0.409

Gnomad4 NFE AF: 0.307

Gnomad4 OTH AF: 0.413

Alfa AF: 0.224 Hom.: 502

Bravo AF: 0.446

Asia WGS AF: 0.539 AC: 1873 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.45
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs674696; hg19: chr21-46179598; COSMIC: COSV65961935;