17-75589380-T-G

Position:

• chr17-75589380-T-G

Variant summary

Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_Strong BP6_Moderate BP7

The NM_001395058.1(MYO15B):​c.1323T>G​(p.Gly441=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.0040 (0 hom., cov: 19)
  • Exomes 𝑓: 0.0000068 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: MYO15B NM_001395058.1 synonymous
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.27

Genes affected

MYO15B (HGNC:14083): (myosin XVB) Predicted to enable ATP binding activity; actin binding activity; and cytoskeletal motor activity. Predicted to be located in brush border; cytoplasm; and cytoskeleton. Predicted to be part of myosin complex. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -7 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BP6: Variant 17-75589380-T-G is Benign according to our data. Variant chr17-75589380-T-G is described in ClinVar as [Likely_benign]. Clinvar id is 2648265.Status of the report is criteria_provided_single_submitter, 1 stars.
• BP7: Synonymous conserved (PhyloP=-1.27 with no splicing effect.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MYO15B	NM_001395058.1	c.1323T>G	p.Gly441=	synonymous_variant	1/64	ENST00000645453.3	NP_001381987.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MYO15B	ENST00000645453.3	c.1323T>G	p.Gly441=	synonymous_variant	1/64		NM_001395058.1	ENSP00000495242	P1

Frequencies

GnomAD3 genomes AF: 0.00 AC: 267 AN: 66724 Hom.: 0 Cov.: 19 FAILED QC

Gnomad AFR AF: 0.00358

Gnomad AMI AF: 0.0101

Gnomad AMR AF: 0.00266

Gnomad ASJ AF: 0.00163

Gnomad EAS AF: 0.00235

Gnomad SAS AF: 0.00514

Gnomad FIN AF: 0.00304

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00474

Gnomad OTH AF: 0.00332

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00000682 AC: 1 AN: 146588 Hom.: 0 Cov.: 0 AF XY: 0.0000134 AC XY: 1 AN XY: 74408

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.000448

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.00400 AC: 267 AN: 66772 Hom.: 0 Cov.: 19 AF XY: 0.00385 AC XY: 124 AN XY: 32170

Gnomad4 AFR AF: 0.00357

Gnomad4 AMR AF: 0.00266

Gnomad4 ASJ AF: 0.00163

Gnomad4 EAS AF: 0.00236

Gnomad4 SAS AF: 0.00519

Gnomad4 FIN AF: 0.00304

Gnomad4 NFE AF: 0.00474

Gnomad4 OTH AF: 0.00329

Alfa AF: 0.0597 Hom.: 7

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

CeGaT Center for Human Genetics Tuebingen

Oct 01, 2022

MYO15B: BP4, BP7 -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	5.7
DANN	Benign	0.61

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: rs181867719; hg19: chr17-73585461;