rs4130603

Variant names:

• chr11-33844336-G-A
• rs4130603

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 0.0286 in 152,256 control chromosomes in the GnomAD database, including 136 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 0.029 (136 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.124
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0716 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: 0.0287 AC: 4361 AN: 152138 Hom.: 135 Cov.: 32

Gnomad AFR AF: 0.0739

Gnomad AMI AF: 0.00768

Gnomad AMR AF: 0.0133

Gnomad ASJ AF: 0.00691

Gnomad EAS AF: 0.0691

Gnomad SAS AF: 0.0116

Gnomad FIN AF: 0.00358

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.00804

Gnomad OTH AF: 0.0248

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

GnomAD4 genome AF: 0.0286 AC: 4360 AN: 152256 Hom.: 136 Cov.: 32 AF XY: 0.0281 AC XY: 2094 AN XY: 74446

African (AFR) AF: 0.0738 AC: 3065 AN: 41540

American (AMR) AF: 0.0133 AC: 203 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.00691 AC: 24 AN: 3472

East Asian (EAS) AF: 0.0694 AC: 360 AN: 5184

South Asian (SAS) AF: 0.0116 AC: 56 AN: 4828

European-Finnish (FIN) AF: 0.00358 AC: 38 AN: 10606

Middle Eastern (MID) AF: 0.0340 AC: 10 AN: 294

European-Non Finnish (NFE) AF: 0.00804 AC: 547 AN: 68018

Other (OTH) AF: 0.0236 AC: 50 AN: 2116

Alfa AF: 0.0202 Hom.: 117

Bravo AF: 0.0313

Asia WGS AF: 0.0530 AC: 184 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.1
DANN	Benign	0.68
PhyloP100		0.12

Splicing

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

Other links and lift over

dbSNP: rs4130603; hg19: chr11-33865882;