rs11245788

Positions:

• chr11-50154550-C-G
• chr11-50154550-C-T

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 0.354 in 151,774 control chromosomes in the GnomAD database, including 11,741 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 0.35 (11741 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.556

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.499 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: 0.354 AC: 53638 AN: 151656 Hom.: 11732 Cov.: 32

Gnomad AFR AF: 0.0894

Gnomad AMI AF: 0.570

Gnomad AMR AF: 0.509

Gnomad ASJ AF: 0.565

Gnomad EAS AF: 0.319

Gnomad SAS AF: 0.298

Gnomad FIN AF: 0.469

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.453

Gnomad OTH AF: 0.413

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

GnomAD4 genome AF: 0.354 AC: 53660 AN: 151774 Hom.: 11741 Cov.: 32 AF XY: 0.355 AC XY: 26360 AN XY: 74172

Gnomad4 AFR AF: 0.0891

Gnomad4 AMR AF: 0.509

Gnomad4 ASJ AF: 0.565

Gnomad4 EAS AF: 0.319

Gnomad4 SAS AF: 0.300

Gnomad4 FIN AF: 0.469

Gnomad4 NFE AF: 0.453

Gnomad4 OTH AF: 0.417

Alfa AF: 0.398 Hom.: 1686

Bravo AF: 0.349

Asia WGS AF: 0.299 AC: 1039 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.36
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11245788; hg19: chr11-50113721;