rs7120258

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PRR33	XM_047426236.1	c.-10+346G>T		intron_variant	Intron 1 of 1		XP_047282192.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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 v4.3

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;