rs916111

Positions:

• chr11-5248113-T-A
• chr11-5248113-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 0.472 in 513,726 control chromosomes in the GnomAD database, including 60,838 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 0.43 (15347 hom., cov: 33)
  • Exomes 𝑓: 0.49 (45491 hom.)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.689

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.754 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: 0.425 AC: 64574 AN: 151906 Hom.: 15333 Cov.: 33

Gnomad AFR AF: 0.222

Gnomad AMI AF: 0.520

Gnomad AMR AF: 0.570

Gnomad ASJ AF: 0.621

Gnomad EAS AF: 0.774

Gnomad SAS AF: 0.535

Gnomad FIN AF: 0.461

Gnomad MID AF: 0.608

Gnomad NFE AF: 0.462

Gnomad OTH AF: 0.485

GnomAD4 exome AF: 0.492 AC: 178087 AN: 361702 Hom.: 45491 Cov.: 4 AF XY: 0.496 AC XY: 95877 AN XY: 193368

Gnomad4 AFR exome AF: 0.222

Gnomad4 AMR exome AF: 0.592

Gnomad4 ASJ exome AF: 0.620

Gnomad4 EAS exome AF: 0.729

Gnomad4 SAS exome AF: 0.531

Gnomad4 FIN exome AF: 0.464

Gnomad4 NFE exome AF: 0.462

Gnomad4 OTH exome AF: 0.496

GnomAD4 genome AF: 0.425 AC: 64628 AN: 152024 Hom.: 15347 Cov.: 33 AF XY: 0.432 AC XY: 32059 AN XY: 74284

Gnomad4 AFR AF: 0.222

Gnomad4 AMR AF: 0.571

Gnomad4 ASJ AF: 0.621

Gnomad4 EAS AF: 0.774

Gnomad4 SAS AF: 0.537

Gnomad4 FIN AF: 0.461

Gnomad4 NFE AF: 0.462

Gnomad4 OTH AF: 0.488

Alfa AF: 0.430 Hom.: 1838

Bravo AF: 0.422

Asia WGS AF: 0.594 AC: 2067 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.5
DANN	Benign	0.56
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs916111; hg19: chr11-5269343;