Variant 17-75610953-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2

The NM_001395058.1(MYO15B):c.4440A>G(p.Pro1480Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00143 in 702,972 control chromosomes in the GnomAD database, including 5 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0013 ( 1 hom., cov: 31)

Exomes 𝑓: 0.0015 ( 4 hom. )

Consequence

MYO15B
NM_001395058.1 synonymous

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.236

Variant links:

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]

MYO15B links:

MYO15B (HGNC:):

MYO15B links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -15 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.65).

BP6

Variant 17-75610953-A-G is Benign according to our data. Variant chr17-75610953-A-G is described in ClinVar as [Likely_benign]. Clinvar id is 2648271.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=-0.236 with no splicing effect.

BS1

Variant frequency is greater than expected in population mid. gnomad4_exome allele frequency = 0.00146 (802/550744) while in subpopulation MID AF= 0.0253 (103/4072). AF 95% confidence interval is 0.0213. There are 4 homozygotes in gnomad4_exome. There are 445 alleles in male gnomad4_exome subpopulation. Median coverage is 0. This position pass quality control queck.

BS2

High Homozygotes in GnomAdExome4 at 4 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MYO15B	NM_001395058.1 linkuse as main transcript	c.4440A>G	p.Pro1480Pro	synonymous_variant	23/64	ENST00000645453.3	NP_001381987.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MYO15B	ENST00000645453.3 linkuse as main transcript	c.4440A>G	p.Pro1480Pro	synonymous_variant	23/64		NM_001395058.1	ENSP00000495242.3		A0A2R8YFM0

Frequencies

GnomAD3 genomes

AF:

0.00134

AC:

204

AN:

152110

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00106

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00465

Gnomad ASJ

AF:

0.00432

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00145

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.0127

Gnomad NFE

AF:

0.000853

Gnomad OTH

AF:

0.00239

GnomAD3 exomes

AF:

0.00189

AC:

259

AN:

137248

Hom.:

AF XY:

0.00205

AC XY:

153

AN XY:

74548

show subpopulations

Gnomad AFR exome

AF:

0.000308

Gnomad AMR exome

AF:

0.00323

Gnomad ASJ exome

AF:

0.00590

Gnomad EAS exome

AF:

0.0000952

Gnomad SAS exome

AF:

0.00200

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.00108

Gnomad OTH exome

AF:

0.00593

GnomAD4 exome

AF:

0.00146

AC:

802

AN:

550744

Hom.:

Cov.:

AF XY:

0.00149

AC XY:

445

AN XY:

298146

show subpopulations

Gnomad4 AFR exome

AF:

0.00114

Gnomad4 AMR exome

AF:

0.00320

Gnomad4 ASJ exome

AF:

0.00529

Gnomad4 EAS exome

AF:

0.0000311

Gnomad4 SAS exome

AF:

0.00201

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.000811

Gnomad4 OTH exome

AF:

0.00261

GnomAD4 genome

AF:

0.00134

AC:

204

AN:

152228

Hom.:

Cov.:

AF XY:

0.00132

AC XY:

AN XY:

74426

show subpopulations

Gnomad4 AFR

AF:

0.00106

Gnomad4 AMR

AF:

0.00464

Gnomad4 ASJ

AF:

0.00432

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00145

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.000853

Gnomad4 OTH

AF:

0.00237

Alfa

AF:

0.00269

Hom.:

Bravo

AF:

0.00213

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Feb 01, 2023

MYO15B: BP4, BP7, BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.65

CADD

Benign

4.6

DANN

Benign

0.86

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over