21-23156493-T-C

Position:

• chr21-23156493-T-C

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 0.134 in 151,752 control chromosomes in the GnomAD database, including 1,443 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 0.13 (1443 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.255

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.16 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: 0.134 AC: 20390 AN: 151638 Hom.: 1443 Cov.: 32

Gnomad AFR AF: 0.0913

Gnomad AMI AF: 0.127

Gnomad AMR AF: 0.135

Gnomad ASJ AF: 0.124

Gnomad EAS AF: 0.108

Gnomad SAS AF: 0.169

Gnomad FIN AF: 0.154

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.157

Gnomad OTH AF: 0.141

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

GnomAD4 genome AF: 0.134 AC: 20392 AN: 151752 Hom.: 1443 Cov.: 32 AF XY: 0.137 AC XY: 10145 AN XY: 74156

Gnomad4 AFR AF: 0.0913

Gnomad4 AMR AF: 0.135

Gnomad4 ASJ AF: 0.124

Gnomad4 EAS AF: 0.108

Gnomad4 SAS AF: 0.169

Gnomad4 FIN AF: 0.154

Gnomad4 NFE AF: 0.157

Gnomad4 OTH AF: 0.140

Alfa AF: 0.153 Hom.: 749

Bravo AF: 0.128

Asia WGS AF: 0.130 AC: 450 AN: 3460

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.8
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1395087; hg19: chr21-24528815;