21-31068221-T-C

Position:

• chr21-31068221-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 0.848 in 152,232 control chromosomes in the GnomAD database, including 56,781 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 0.85 (56781 hom., cov: 33)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.41

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.95 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.31068221T>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.849 AC: 129075 AN: 152114 Hom.: 56772 Cov.: 33

Gnomad AFR AF: 0.587

Gnomad AMI AF: 0.970

Gnomad AMR AF: 0.923

Gnomad ASJ AF: 0.940

Gnomad EAS AF: 0.917

Gnomad SAS AF: 0.898

Gnomad FIN AF: 0.964

Gnomad MID AF: 0.949

Gnomad NFE AF: 0.956

Gnomad OTH AF: 0.883

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

GnomAD4 genome AF: 0.848 AC: 129120 AN: 152232 Hom.: 56781 Cov.: 33 AF XY: 0.850 AC XY: 63247 AN XY: 74436

Gnomad4 AFR AF: 0.586

Gnomad4 AMR AF: 0.923

Gnomad4 ASJ AF: 0.940

Gnomad4 EAS AF: 0.917

Gnomad4 SAS AF: 0.899

Gnomad4 FIN AF: 0.964

Gnomad4 NFE AF: 0.956

Gnomad4 OTH AF: 0.883

Alfa AF: 0.944 Hom.: 116228

Bravo AF: 0.837

Asia WGS AF: 0.893 AC: 3105 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.032
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1475591; hg19: chr21-32440540;