rs2830495

Positions:

• chr21-26781140-C-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 0.0704 in 152,128 control chromosomes in the GnomAD database, including 491 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 0.070 (491 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.418

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 = 0.116 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: 0.0703 AC: 10693 AN: 152010 Hom.: 490 Cov.: 31

Gnomad AFR AF: 0.119

Gnomad AMI AF: 0.0811

Gnomad AMR AF: 0.0530

Gnomad ASJ AF: 0.0162

Gnomad EAS AF: 0.0903

Gnomad SAS AF: 0.0476

Gnomad FIN AF: 0.0248

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0548

Gnomad OTH AF: 0.0627

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

GnomAD4 genome AF: 0.0704 AC: 10711 AN: 152128 Hom.: 491 Cov.: 31 AF XY: 0.0678 AC XY: 5040 AN XY: 74376

Gnomad4 AFR AF: 0.119

Gnomad4 AMR AF: 0.0530

Gnomad4 ASJ AF: 0.0162

Gnomad4 EAS AF: 0.0903

Gnomad4 SAS AF: 0.0473

Gnomad4 FIN AF: 0.0248

Gnomad4 NFE AF: 0.0548

Gnomad4 OTH AF: 0.0616

Alfa AF: 0.0569 Hom.: 140

Bravo AF: 0.0737

Asia WGS AF: 0.0520 AC: 180 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.22
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2830495; hg19: chr21-28153459;