21-25214010-A-G

Position:

• chr21-25214010-A-G

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 0.0589 in 152,132 control chromosomes in the GnomAD database, including 308 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 0.059 (308 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.266

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.153 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.25214010A>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000222042	ENST00000409758.1	n.90-38565T>C		intron_variant		3
ENSG00000222042	ENST00000656005.1	n.218-38565T>C		intron_variant
ENSG00000222042	ENST00000667825.1	n.190-38565T>C		intron_variant

Frequencies

GnomAD3 genomes AF: 0.0589 AC: 8955 AN: 152014 Hom.: 309 Cov.: 32

Gnomad AFR AF: 0.0423

Gnomad AMI AF: 0.0164

Gnomad AMR AF: 0.0376

Gnomad ASJ AF: 0.0764

Gnomad EAS AF: 0.137

Gnomad SAS AF: 0.163

Gnomad FIN AF: 0.0479

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0619

Gnomad OTH AF: 0.0574

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

GnomAD4 genome AF: 0.0589 AC: 8953 AN: 152132 Hom.: 308 Cov.: 32 AF XY: 0.0598 AC XY: 4450 AN XY: 74368

Gnomad4 AFR AF: 0.0422

Gnomad4 AMR AF: 0.0376

Gnomad4 ASJ AF: 0.0764

Gnomad4 EAS AF: 0.136

Gnomad4 SAS AF: 0.162

Gnomad4 FIN AF: 0.0479

Gnomad4 NFE AF: 0.0619

Gnomad4 OTH AF: 0.0596

Alfa AF: 0.0624 Hom.: 464

Bravo AF: 0.0545

Asia WGS AF: 0.166 AC: 577 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	4.9
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: rs2829644; hg19: chr21-26586324;