rs2096911

Positions:

• chr21-23183771-C-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 0.358 in 151,978 control chromosomes in the GnomAD database, including 11,601 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 0.36 (11601 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.45

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.06).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.457 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: 0.358 AC: 54408 AN: 151862 Hom.: 11603 Cov.: 31

Gnomad AFR AF: 0.135

Gnomad AMI AF: 0.595

Gnomad AMR AF: 0.415

Gnomad ASJ AF: 0.484

Gnomad EAS AF: 0.217

Gnomad SAS AF: 0.376

Gnomad FIN AF: 0.490

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.461

Gnomad OTH AF: 0.356

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

GnomAD4 genome AF: 0.358 AC: 54395 AN: 151978 Hom.: 11601 Cov.: 31 AF XY: 0.360 AC XY: 26729 AN XY: 74266

Gnomad4 AFR AF: 0.135

Gnomad4 AMR AF: 0.414

Gnomad4 ASJ AF: 0.484

Gnomad4 EAS AF: 0.217

Gnomad4 SAS AF: 0.376

Gnomad4 FIN AF: 0.490

Gnomad4 NFE AF: 0.461

Gnomad4 OTH AF: 0.353

Alfa AF: 0.409 Hom.: 1738

Bravo AF: 0.343

Asia WGS AF: 0.291 AC: 1013 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.13
DANN	Benign	0.15

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2096911; hg19: chr21-24556093;