rs4130603

Positions:

• chr11-33844336-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 0.0286 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.0738

Gnomad4 AMR AF: 0.0133

Gnomad4 ASJ AF: 0.00691

Gnomad4 EAS AF: 0.0694

Gnomad4 SAS AF: 0.0116

Gnomad4 FIN AF: 0.00358

Gnomad4 NFE AF: 0.00804

Gnomad4 OTH AF: 0.0236

Alfa AF: 0.0129 Hom.: 34

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4130603; hg19: chr11-33865882;