rs4987059

Positions:

• chr11-636433-G-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 0.0517 in 152,256 control chromosomes in the GnomAD database, including 224 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 0.052 (224 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.261

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0606 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: 0.0516 AC: 7852 AN: 152138 Hom.: 224 Cov.: 33

Gnomad AFR AF: 0.0624

Gnomad AMI AF: 0.0440

Gnomad AMR AF: 0.0412

Gnomad ASJ AF: 0.130

Gnomad EAS AF: 0.0133

Gnomad SAS AF: 0.0318

Gnomad FIN AF: 0.0391

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.0491

Gnomad OTH AF: 0.0656

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

GnomAD4 genome AF: 0.0517 AC: 7867 AN: 152256 Hom.: 224 Cov.: 33 AF XY: 0.0509 AC XY: 3788 AN XY: 74460

Gnomad4 AFR AF: 0.0626

Gnomad4 AMR AF: 0.0411

Gnomad4 ASJ AF: 0.130

Gnomad4 EAS AF: 0.0135

Gnomad4 SAS AF: 0.0317

Gnomad4 FIN AF: 0.0391

Gnomad4 NFE AF: 0.0491

Gnomad4 OTH AF: 0.0668

Alfa AF: 0.0515 Hom.: 56

Bravo AF: 0.0533

Asia WGS AF: 0.0240 AC: 85 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.7
DANN	Benign	0.90

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4987059; hg19: chr11-636433;