21-29190676-A-T

Variant names:

• chr21-29190676-A-T
• rs2832253

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;