rs11820646

chr11-129591276-T-Cchr11-129591276-T-G

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 0.644 in 151,964 control chromosomes in the GnomAD database, including 32,114 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 0.64 (32114 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.494

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.765 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: 0.643 AC: 97708 AN: 151846 Hom.: 32078 Cov.: 31

Gnomad AFR AF: 0.772

Gnomad AMI AF: 0.620

Gnomad AMR AF: 0.596

Gnomad ASJ AF: 0.644

Gnomad EAS AF: 0.535

Gnomad SAS AF: 0.686

Gnomad FIN AF: 0.518

Gnomad MID AF: 0.652

Gnomad NFE AF: 0.601

Gnomad OTH AF: 0.654

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

GnomAD4 genome AF: 0.644 AC: 97801 AN: 151964 Hom.: 32114 Cov.: 31 AF XY: 0.640 AC XY: 47513 AN XY: 74252

Gnomad4 AFR AF: 0.772

Gnomad4 AMR AF: 0.596

Gnomad4 ASJ AF: 0.644

Gnomad4 EAS AF: 0.534

Gnomad4 SAS AF: 0.687

Gnomad4 FIN AF: 0.518

Gnomad4 NFE AF: 0.601

Gnomad4 OTH AF: 0.653

Alfa AF: 0.581 Hom.: 5240

Bravo AF: 0.650

Asia WGS AF: 0.643 AC: 2233 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	0.83
Dann	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11820646; hg19: chr11-129461171;