rs4987059

Variant names:

• chr11-636433-G-A
• rs4987059

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 7 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.0626 AC: 2601 AN: 41548

American (AMR) AF: 0.0411 AC: 629 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.130 AC: 450 AN: 3470

East Asian (EAS) AF: 0.0135 AC: 70 AN: 5186

South Asian (SAS) AF: 0.0317 AC: 153 AN: 4832

European-Finnish (FIN) AF: 0.0391 AC: 415 AN: 10614

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.0491 AC: 3340 AN: 68004

Other (OTH) AF: 0.0668 AC: 141 AN: 2112

Alfa AF: 0.0497 Hom.: 345

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
PhyloP100		-0.26

Splicing

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

Other links and lift over

dbSNP: rs4987059; hg19: chr11-636433;