rs11088976

chr21-44989634-A-Gchr21-44989634-A-Tchr21-44989634-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 0.72 in 152,142 control chromosomes in the GnomAD database, including 40,369 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 0.72 (40369 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.38

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.809 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: 0.720 AC: 109479 AN: 152024 Hom.: 40361 Cov.: 34

Gnomad AFR AF: 0.554

Gnomad AMI AF: 0.749

Gnomad AMR AF: 0.779

Gnomad ASJ AF: 0.769

Gnomad EAS AF: 0.830

Gnomad SAS AF: 0.820

Gnomad FIN AF: 0.789

Gnomad MID AF: 0.744

Gnomad NFE AF: 0.779

Gnomad OTH AF: 0.732

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

GnomAD4 genome AF: 0.720 AC: 109521 AN: 152142 Hom.: 40369 Cov.: 34 AF XY: 0.723 AC XY: 53810 AN XY: 74384

Gnomad4 AFR AF: 0.553

Gnomad4 AMR AF: 0.779

Gnomad4 ASJ AF: 0.769

Gnomad4 EAS AF: 0.830

Gnomad4 SAS AF: 0.821

Gnomad4 FIN AF: 0.789

Gnomad4 NFE AF: 0.778

Gnomad4 OTH AF: 0.734

Alfa AF: 0.706 Hom.: 2540

Bravo AF: 0.709

Asia WGS AF: 0.814 AC: 2827 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	0.74
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: rs11088976; hg19: chr21-46409549;