11-1917293-C-A

Variant names:

• chr11-1917293-C-A
• rs7120258
• XM_047426236.1:c.-10+346G>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XM_047426236.1(PRR33):​c.-10+346G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.107 in 152,204 control chromosomes in the GnomAD database, including 984 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 0.11 (984 hom., cov: 33)
• Consequence: PRR33 XM_047426236.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.538
• Publications: 6 publications found

Genes affected

PRR33 (HGNC:35118): (proline rich 33) Predicted to act upstream of or within response to wounding. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.154 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.107 AC: 16272 AN: 152084 Hom.: 982 Cov.: 33

Gnomad AFR AF: 0.157

Gnomad AMI AF: 0.114

Gnomad AMR AF: 0.0726

Gnomad ASJ AF: 0.0602

Gnomad EAS AF: 0.110

Gnomad SAS AF: 0.120

Gnomad FIN AF: 0.0871

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.0878

Gnomad OTH AF: 0.118

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

GnomAD4 genome AF: 0.107 AC: 16285 AN: 152204 Hom.: 984 Cov.: 33 AF XY: 0.107 AC XY: 7977 AN XY: 74418

African (AFR) AF: 0.157 AC: 6519 AN: 41528

American (AMR) AF: 0.0725 AC: 1109 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.0602 AC: 209 AN: 3470

East Asian (EAS) AF: 0.111 AC: 572 AN: 5164

South Asian (SAS) AF: 0.120 AC: 581 AN: 4828

European-Finnish (FIN) AF: 0.0871 AC: 924 AN: 10612

Middle Eastern (MID) AF: 0.180 AC: 53 AN: 294

European-Non Finnish (NFE) AF: 0.0877 AC: 5964 AN: 67982

Other (OTH) AF: 0.119 AC: 250 AN: 2108

Alfa AF: 0.0901 Hom.: 580

Bravo AF: 0.108

Asia WGS AF: 0.0980 AC: 340 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	12
DANN	Benign	0.65
PhyloP100		0.54

Splicing

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

Other links and lift over

dbSNP: rs7120258; hg19: chr11-1938523;