chr21-42308924-C-T

Position:

• chr21-42308924-C-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 0.603 in 152,158 control chromosomes in the GnomAD database, including 29,767 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 0.60 (29767 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.529

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.83 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: 0.603 AC: 91632 AN: 152040 Hom.: 29727 Cov.: 32

Gnomad AFR AF: 0.837

Gnomad AMI AF: 0.647

Gnomad AMR AF: 0.519

Gnomad ASJ AF: 0.596

Gnomad EAS AF: 0.188

Gnomad SAS AF: 0.447

Gnomad FIN AF: 0.485

Gnomad MID AF: 0.623

Gnomad NFE AF: 0.539

Gnomad OTH AF: 0.592

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

GnomAD4 genome AF: 0.603 AC: 91732 AN: 152158 Hom.: 29767 Cov.: 32 AF XY: 0.594 AC XY: 44156 AN XY: 74384

Gnomad4 AFR AF: 0.837

Gnomad4 AMR AF: 0.519

Gnomad4 ASJ AF: 0.596

Gnomad4 EAS AF: 0.188

Gnomad4 SAS AF: 0.447

Gnomad4 FIN AF: 0.485

Gnomad4 NFE AF: 0.539

Gnomad4 OTH AF: 0.591

Alfa AF: 0.552 Hom.: 18725

Bravo AF: 0.615

Asia WGS AF: 0.359 AC: 1246 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.0
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs225436; hg19: chr21-43729034;