11-60011390-T-G

Variant names:

• chr11-60011390-T-G
• rs602041
• ENST00000644647.1:n.142-281T>G

Variant summary

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

The ENST00000644647.1(OOSP4B):​n.142-281T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.222 in 151,926 control chromosomes in the GnomAD database, including 4,302 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 0.22 (4302 hom., cov: 32)
• Consequence: OOSP4B ENST00000644647.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.628
• Publications: 3 publications found

Genes affected

OOSP4B (HGNC:53905): (oocyte secreted protein family member 4B) Predicted to be located in extracellular region. [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=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.463 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
OOSP4B	ENST00000644647.1	n.142-281T>G		intron_variant	Intron 1 of 9

Frequencies

GnomAD3 genomes AF: 0.222 AC: 33679 AN: 151808 Hom.: 4295 Cov.: 32

Gnomad AFR AF: 0.297

Gnomad AMI AF: 0.181

Gnomad AMR AF: 0.202

Gnomad ASJ AF: 0.154

Gnomad EAS AF: 0.479

Gnomad SAS AF: 0.342

Gnomad FIN AF: 0.115

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.173

Gnomad OTH AF: 0.226

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

GnomAD4 genome AF: 0.222 AC: 33719 AN: 151926 Hom.: 4302 Cov.: 32 AF XY: 0.224 AC XY: 16612 AN XY: 74266

African (AFR) AF: 0.297 AC: 12319 AN: 41414

American (AMR) AF: 0.202 AC: 3075 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.154 AC: 535 AN: 3468

East Asian (EAS) AF: 0.479 AC: 2467 AN: 5152

South Asian (SAS) AF: 0.340 AC: 1640 AN: 4818

European-Finnish (FIN) AF: 0.115 AC: 1215 AN: 10598

Middle Eastern (MID) AF: 0.133 AC: 39 AN: 294

European-Non Finnish (NFE) AF: 0.173 AC: 11773 AN: 67932

Other (OTH) AF: 0.233 AC: 491 AN: 2110

Alfa AF: 0.123 Hom.: 260

Bravo AF: 0.230

Asia WGS AF: 0.433 AC: 1504 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.1
DANN	Benign	0.70
PhyloP100		-0.63

Splicing

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

Other links and lift over

dbSNP: rs602041; hg19: chr11-59778863;