rs75915166

chr11-69564393-C-A

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 0.0397 in 152,260 control chromosomes in the GnomAD database, including 180 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 0.040 (180 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.252

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0858 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: 0.0397 AC: 6041 AN: 152142 Hom.: 181 Cov.: 32

Gnomad AFR AF: 0.00985

Gnomad AMI AF: 0.0197

Gnomad AMR AF: 0.0353

Gnomad ASJ AF: 0.0303

Gnomad EAS AF: 0.00212

Gnomad SAS AF: 0.0926

Gnomad FIN AF: 0.0350

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0596

Gnomad OTH AF: 0.0382

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

GnomAD4 genome AF: 0.0397 AC: 6044 AN: 152260 Hom.: 180 Cov.: 32 AF XY: 0.0397 AC XY: 2956 AN XY: 74460

Gnomad4 AFR AF: 0.00982

Gnomad4 AMR AF: 0.0352

Gnomad4 ASJ AF: 0.0303

Gnomad4 EAS AF: 0.00212

Gnomad4 SAS AF: 0.0929

Gnomad4 FIN AF: 0.0350

Gnomad4 NFE AF: 0.0596

Gnomad4 OTH AF: 0.0392

Alfa AF: 0.0542 Hom.: 67

Bravo AF: 0.0357

Asia WGS AF: 0.0590 AC: 206 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	2.5
Dann	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs75915166; hg19: chr11-69379161;