21-30260607-A-T

Position:

• chr21-30260607-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 0.841 in 152,128 control chromosomes in the GnomAD database, including 54,202 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 0.84 (54202 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.49

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.93 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: 0.841 AC: 127880 AN: 152010 Hom.: 54138 Cov.: 32

Gnomad AFR AF: 0.937

Gnomad AMI AF: 0.874

Gnomad AMR AF: 0.839

Gnomad ASJ AF: 0.812

Gnomad EAS AF: 0.857

Gnomad SAS AF: 0.883

Gnomad FIN AF: 0.752

Gnomad MID AF: 0.854

Gnomad NFE AF: 0.794

Gnomad OTH AF: 0.828

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

GnomAD4 genome AF: 0.841 AC: 128002 AN: 152128 Hom.: 54202 Cov.: 32 AF XY: 0.841 AC XY: 62544 AN XY: 74368

Gnomad4 AFR AF: 0.938

Gnomad4 AMR AF: 0.839

Gnomad4 ASJ AF: 0.812

Gnomad4 EAS AF: 0.856

Gnomad4 SAS AF: 0.883

Gnomad4 FIN AF: 0.752

Gnomad4 NFE AF: 0.794

Gnomad4 OTH AF: 0.827

Alfa AF: 0.824 Hom.: 6444

Bravo AF: 0.850

Asia WGS AF: 0.872 AC: 3033 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.28
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs996610; hg19: chr21-31632925;