21-41411121-T-C

Variant names:

• chr21-41411121-T-C
• rs464090

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 0.712 in 152,104 control chromosomes in the GnomAD database, including 39,650 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 0.71 (39650 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.792

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.802 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: 0.713 AC: 108356 AN: 151986 Hom.: 39658 Cov.: 31

Gnomad AFR AF: 0.547

Gnomad AMI AF: 0.781

Gnomad AMR AF: 0.709

Gnomad ASJ AF: 0.768

Gnomad EAS AF: 0.602

Gnomad SAS AF: 0.590

Gnomad FIN AF: 0.837

Gnomad MID AF: 0.807

Gnomad NFE AF: 0.808

Gnomad OTH AF: 0.715

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

GnomAD4 genome AF: 0.712 AC: 108368 AN: 152104 Hom.: 39650 Cov.: 31 AF XY: 0.712 AC XY: 52935 AN XY: 74368

Gnomad4 AFR AF: 0.546

Gnomad4 AMR AF: 0.708

Gnomad4 ASJ AF: 0.768

Gnomad4 EAS AF: 0.602

Gnomad4 SAS AF: 0.592

Gnomad4 FIN AF: 0.837

Gnomad4 NFE AF: 0.808

Gnomad4 OTH AF: 0.713

Alfa AF: 0.660 Hom.: 2678

Bravo AF: 0.699

Asia WGS AF: 0.592 AC: 2056 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.4
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs464090; hg19: chr21-42783048;