21-29190676-A-T

Position:

• chr21-29190676-A-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 0.068 in 152,292 control chromosomes in the GnomAD database, including 471 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 0.068 (471 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.147

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.101 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: 0.0681 AC: 10356 AN: 152174 Hom.: 471 Cov.: 33

Gnomad AFR AF: 0.0205

Gnomad AMI AF: 0.0318

Gnomad AMR AF: 0.0559

Gnomad ASJ AF: 0.103

Gnomad EAS AF: 0.000961

Gnomad SAS AF: 0.0565

Gnomad FIN AF: 0.0762

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.103

Gnomad OTH AF: 0.0807

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

GnomAD4 genome AF: 0.0680 AC: 10353 AN: 152292 Hom.: 471 Cov.: 33 AF XY: 0.0649 AC XY: 4833 AN XY: 74468

Gnomad4 AFR AF: 0.0204

Gnomad4 AMR AF: 0.0558

Gnomad4 ASJ AF: 0.103

Gnomad4 EAS AF: 0.000963

Gnomad4 SAS AF: 0.0570

Gnomad4 FIN AF: 0.0762

Gnomad4 NFE AF: 0.103

Gnomad4 OTH AF: 0.0799

Alfa AF: 0.0429 Hom.: 32

Bravo AF: 0.0644

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	8.1
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: rs2832253; hg19: chr21-30562997;