rs11088680

Positions:

• chr21-13514758-A-G
• chr21-13514758-A-T
• chr21-13514758-A-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 0.308 in 151,234 control chromosomes in the GnomAD database, including 9,026 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 0.31 (9026 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.875

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.861 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: 0.307 AC: 46459 AN: 151116 Hom.: 9015 Cov.: 30

Gnomad AFR AF: 0.451

Gnomad AMI AF: 0.101

Gnomad AMR AF: 0.262

Gnomad ASJ AF: 0.265

Gnomad EAS AF: 0.883

Gnomad SAS AF: 0.383

Gnomad FIN AF: 0.216

Gnomad MID AF: 0.377

Gnomad NFE AF: 0.202

Gnomad OTH AF: 0.314

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

GnomAD4 genome AF: 0.308 AC: 46508 AN: 151234 Hom.: 9026 Cov.: 30 AF XY: 0.311 AC XY: 22996 AN XY: 73890

Gnomad4 AFR AF: 0.451

Gnomad4 AMR AF: 0.262

Gnomad4 ASJ AF: 0.265

Gnomad4 EAS AF: 0.882

Gnomad4 SAS AF: 0.384

Gnomad4 FIN AF: 0.216

Gnomad4 NFE AF: 0.202

Gnomad4 OTH AF: 0.319

Alfa AF: 0.252 Hom.: 711

Bravo AF: 0.323

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.8
DANN	Benign	0.28

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11088680; hg19: chr21-14887079;