chr21-27821868-T-C

Position:

• chr21-27821868-T-C

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 0.594 in 152,098 control chromosomes in the GnomAD database, including 26,930 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 0.59 (26930 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.29

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 (AFR) allele frequency at 95% confidence interval = 0.636 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: 0.594 AC: 90264 AN: 151980 Hom.: 26895 Cov.: 33

Gnomad AFR AF: 0.642

Gnomad AMI AF: 0.636

Gnomad AMR AF: 0.622

Gnomad ASJ AF: 0.515

Gnomad EAS AF: 0.579

Gnomad SAS AF: 0.522

Gnomad FIN AF: 0.481

Gnomad MID AF: 0.519

Gnomad NFE AF: 0.587

Gnomad OTH AF: 0.560

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

GnomAD4 genome AF: 0.594 AC: 90360 AN: 152098 Hom.: 26930 Cov.: 33 AF XY: 0.588 AC XY: 43719 AN XY: 74354

Gnomad4 AFR AF: 0.642

Gnomad4 AMR AF: 0.623

Gnomad4 ASJ AF: 0.515

Gnomad4 EAS AF: 0.579

Gnomad4 SAS AF: 0.523

Gnomad4 FIN AF: 0.481

Gnomad4 NFE AF: 0.587

Gnomad4 OTH AF: 0.564

Alfa AF: 0.594 Hom.: 4503

Bravo AF: 0.605

Asia WGS AF: 0.545 AC: 1892 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.72
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs243687; hg19: chr21-29194187;