21-46021401-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 0.43 in 148,084 control chromosomes in the GnomAD database, including 14,793 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 (14793 hom., cov: 26)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.892

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.679 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.430 AC: 63595 AN: 148000 Hom.: 14788 Cov.: 26

Gnomad AFR AF: 0.234

Gnomad AMI AF: 0.604

Gnomad AMR AF: 0.546

Gnomad ASJ AF: 0.526

Gnomad EAS AF: 0.698

Gnomad SAS AF: 0.529

Gnomad FIN AF: 0.505

Gnomad MID AF: 0.503

Gnomad NFE AF: 0.474

Gnomad OTH AF: 0.461

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

GnomAD4 genome AF: 0.430 AC: 63620 AN: 148084 Hom.: 14793 Cov.: 26 AF XY: 0.435 AC XY: 31267 AN XY: 71910

Gnomad4 AFR AF: 0.234

Gnomad4 AMR AF: 0.546

Gnomad4 ASJ AF: 0.526

Gnomad4 EAS AF: 0.698

Gnomad4 SAS AF: 0.530

Gnomad4 FIN AF: 0.505

Gnomad4 NFE AF: 0.474

Gnomad4 OTH AF: 0.465

Alfa AF: 0.465 Hom.: 8612

Bravo AF: 0.423

Asia WGS AF: 0.595 AC: 2069 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.43
Dann	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2839081; hg19: chr21-47441315;