rs4756052

Positions:

• chr11-33830926-G-A
• chr11-33830926-G-C

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 0.238 in 152,160 control chromosomes in the GnomAD database, including 5,699 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 0.24 (5699 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.15

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.335 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: 0.238 AC: 36187 AN: 152042 Hom.: 5703 Cov.: 32

Gnomad AFR AF: 0.0690

Gnomad AMI AF: 0.298

Gnomad AMR AF: 0.253

Gnomad ASJ AF: 0.551

Gnomad EAS AF: 0.00403

Gnomad SAS AF: 0.208

Gnomad FIN AF: 0.233

Gnomad MID AF: 0.456

Gnomad NFE AF: 0.338

Gnomad OTH AF: 0.307

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

GnomAD4 genome AF: 0.238 AC: 36172 AN: 152160 Hom.: 5699 Cov.: 32 AF XY: 0.231 AC XY: 17167 AN XY: 74390

Gnomad4 AFR AF: 0.0688

Gnomad4 AMR AF: 0.253

Gnomad4 ASJ AF: 0.551

Gnomad4 EAS AF: 0.00404

Gnomad4 SAS AF: 0.209

Gnomad4 FIN AF: 0.233

Gnomad4 NFE AF: 0.338

Gnomad4 OTH AF: 0.302

Alfa AF: 0.288 Hom.: 3036

Bravo AF: 0.234

Asia WGS AF: 0.105 AC: 368 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.99
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4756052; hg19: chr11-33852472;