rs2096911

Variant names:

• chr21-23183771-C-A
• rs2096911

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;