17-35148017-G-C

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BS1 BS2

The NM_001267052.2(UNC45B):c.-1+107G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00662 in 515,260 control chromosomes in the GnomAD database, including 57 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.010 (31 hom., cov: 32)
  • Exomes 𝑓: 0.0050 (26 hom.)
• Consequence: UNC45B NM_001267052.2 intron
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.220

Genes affected

UNC45B (HGNC:14304): (unc-45 myosin chaperone B) This gene encodes a co-chaperone required for folding and accumulation of type II myosins. The protein consists of three tetratricopeptide repeat motifs at the N-terminus that form a complex with heat shock protein 90, a central region of unknown function that is conserved in all Unc-45 proteins, and a C-terminal Unc-45/Cro1/She4 domain. The protein is expressed at high levels in striated muscle, where its muscle myosin chaperone activity is dependent on heat shock protein 90 acting as a co-chaperone. A missense mutation in this gene has been associated with cataract development. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Apr 2015]

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BP6: Variant 17-35148017-G-C is Benign according to our data. Variant chr17-35148017-G-C is described in ClinVar as [Likely_benign]. Clinvar id is 1191774.Status of the report is criteria_provided_single_submitter, 1 stars.
• BS1: Variant frequency is greater than expected in population eas. gnomad4 allele frequency = 0.0105 (1597/152342) while in subpopulation EAS AF= 0.039 (202/5186). AF 95% confidence interval is 0.0346. There are 31 homozygotes in gnomad4. There are 811 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High AC in GnomAd at 1589 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
UNC45B	NM_001267052.2	c.-1+107G>C		intron_variant		ENST00000394570.7
UNC45B	NM_001033576.2	c.-4+107G>C		intron_variant
UNC45B	XM_017024234.2	c.-1+107G>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
UNC45B	ENST00000394570.7	c.-1+107G>C		intron_variant		1	NM_001267052.2	P4
UNC45B	ENST00000268876.9	c.-4+107G>C		intron_variant		5		A1

Frequencies

GnomAD3 genomes AF: 0.0104 AC: 1589 AN: 152224 Hom.: 30 Cov.: 32

Gnomad AFR AF: 0.0292

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00360

Gnomad ASJ AF: 0.00518

Gnomad EAS AF: 0.0387

Gnomad SAS AF: 0.0124

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.000426

Gnomad OTH AF: 0.00669

GnomAD4 exome AF: 0.00499 AC: 1812 AN: 362918 Hom.: 26 AF XY: 0.00535 AC XY: 1018 AN XY: 190212

Gnomad4 AFR exome AF: 0.0267

Gnomad4 AMR exome AF: 0.00364

Gnomad4 ASJ exome AF: 0.00399

Gnomad4 EAS exome AF: 0.0318

Gnomad4 SAS exome AF: 0.0113

Gnomad4 FIN exome AF: 0.0000431

Gnomad4 NFE exome AF: 0.000498

Gnomad4 OTH exome AF: 0.00523

GnomAD4 genome AF: 0.0105 AC: 1597 AN: 152342 Hom.: 31 Cov.: 32 AF XY: 0.0109 AC XY: 811 AN XY: 74498

Gnomad4 AFR AF: 0.0292

Gnomad4 AMR AF: 0.00359

Gnomad4 ASJ AF: 0.00518

Gnomad4 EAS AF: 0.0390

Gnomad4 SAS AF: 0.0126

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000426

Gnomad4 OTH AF: 0.00662

Alfa AF: 0.00804 Hom.: 1

Bravo AF: 0.0118

Asia WGS AF: 0.0160 AC: 56 AN: 3478

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Likely benign, criteria provided, single submitter

clinical testing

GeneDx

Feb 24, 2020

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
Cadd	Benign	1.6
Dann	Benign	0.79

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs79383041; hg19: chr17-33475036;