rs17111435

chr11-110574927-A-Gchr11-110574927-A-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 0.0612 in 152,268 control chromosomes in the GnomAD database, including 307 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 0.061 (307 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.49

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 (NFE) allele frequency at 95% confidence interval = 0.0746 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: 0.0612 AC: 9315 AN: 152150 Hom.: 306 Cov.: 33

Gnomad AFR AF: 0.0484

Gnomad AMI AF: 0.139

Gnomad AMR AF: 0.0414

Gnomad ASJ AF: 0.0662

Gnomad EAS AF: 0.0302

Gnomad SAS AF: 0.0581

Gnomad FIN AF: 0.0520

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.0763

Gnomad OTH AF: 0.0522

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

GnomAD4 genome AF: 0.0612 AC: 9320 AN: 152268 Hom.: 307 Cov.: 33 AF XY: 0.0592 AC XY: 4406 AN XY: 74448

Gnomad4 AFR AF: 0.0485

Gnomad4 AMR AF: 0.0412

Gnomad4 ASJ AF: 0.0662

Gnomad4 EAS AF: 0.0305

Gnomad4 SAS AF: 0.0583

Gnomad4 FIN AF: 0.0520

Gnomad4 NFE AF: 0.0763

Gnomad4 OTH AF: 0.0516

Alfa AF: 0.0509 Hom.: 54

Bravo AF: 0.0593

Asia WGS AF: 0.0450 AC: 159 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	9.5
Dann	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17111435; hg19: chr11-110445651;