rs2830713

chr21-27122121-T-Cchr21-27122121-T-A

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 0.771 in 152,164 control chromosomes in the GnomAD database, including 45,562 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 0.77 (45562 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.02

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.843 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.771 AC: 117236 AN: 152046 Hom.: 45514 Cov.: 32

Gnomad AFR AF: 0.850

Gnomad AMI AF: 0.870

Gnomad AMR AF: 0.761

Gnomad ASJ AF: 0.730

Gnomad EAS AF: 0.818

Gnomad SAS AF: 0.788

Gnomad FIN AF: 0.747

Gnomad MID AF: 0.810

Gnomad NFE AF: 0.724

Gnomad OTH AF: 0.772

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

GnomAD4 genome AF: 0.771 AC: 117343 AN: 152164 Hom.: 45562 Cov.: 32 AF XY: 0.774 AC XY: 57559 AN XY: 74390

Gnomad4 AFR AF: 0.850

Gnomad4 AMR AF: 0.761

Gnomad4 ASJ AF: 0.730

Gnomad4 EAS AF: 0.818

Gnomad4 SAS AF: 0.787

Gnomad4 FIN AF: 0.747

Gnomad4 NFE AF: 0.724

Gnomad4 OTH AF: 0.771

Alfa AF: 0.736 Hom.: 83136

Bravo AF: 0.780

Asia WGS AF: 0.812 AC: 2818 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.15
Dann	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2830713; hg19: chr21-28494440;