Variant chr15-71826436-G-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_006901.4(MYO9A):c.*144C>G variant causes a 3 prime UTR change. The variant allele was found at a frequency of 0.24 in 765,274 control chromosomes in the GnomAD database, including 23,133 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.25 ( 4915 hom., cov: 32)

Exomes 𝑓: 0.24 ( 18218 hom. )

Consequence

MYO9A
NM_006901.4 3_prime_UTR

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 3.63

Variant links:

Genes affected

MYO9A (HGNC:7608): (myosin IXA) This gene encodes a member of the myosin superfamily. The protein represents an unconventional myosin; it should not be confused with the conventional non-muscle myosin-9 (MYH9). Unconventional myosins contain the basic domains of conventional myosins and are further distinguished from class members by their tail domains. They function as actin-based molecular motors. Mutations in this gene have been associated with Bardet-Biedl Syndrome. [provided by RefSeq, Dec 2011]

MYO9A links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.79).

BP6

Variant 15-71826436-G-C is Benign according to our data. Variant chr15-71826436-G-C is described in ClinVar as [Benign]. Clinvar id is 1235300.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.399 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MYO9A	NM_006901.4 linkuse as main transcript	c.*144C>G		3_prime_UTR_variant	42/42	ENST00000356056.10

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MYO9A	ENST00000356056.10 linkuse as main transcript	c.*144C>G	3_prime_UTR_variant	42/42	1	NM_006901.4	P2	B2RTY4-1
MYO9A	ENST00000561618.5 linkuse as main transcript	c.*144C>G	3_prime_UTR_variant	19/19	1
MYO9A	ENST00000564571.5 linkuse as main transcript	c.*596C>G	3_prime_UTR_variant	42/42	1		A2
MYO9A	ENST00000568042.5 linkuse as main transcript	c.*144C>G	3_prime_UTR_variant	9/9	5

Frequencies

GnomAD3 genomes

AF:

0.247

AC:

37574

AN:

151968

Hom.:

4906

Cov.:

show subpopulations

Gnomad AFR

AF:

0.257

Gnomad AMI

AF:

0.226

Gnomad AMR

AF:

0.290

Gnomad ASJ

AF:

0.197

Gnomad EAS

AF:

0.414

Gnomad SAS

AF:

0.257

Gnomad FIN

AF:

0.240

Gnomad MID

AF:

0.212

Gnomad NFE

AF:

0.222

Gnomad OTH

AF:

0.243

GnomAD4 exome

AF:

0.238

AC:

145725

AN:

613188

Hom.:

18218

Cov.:

AF XY:

0.237

AC XY:

74045

AN XY:

312806

show subpopulations

Gnomad4 AFR exome

AF:

0.256

Gnomad4 AMR exome

AF:

0.309

Gnomad4 ASJ exome

AF:

0.186

Gnomad4 EAS exome

AF:

0.376

Gnomad4 SAS exome

AF:

0.248

Gnomad4 FIN exome

AF:

0.234

Gnomad4 NFE exome

AF:

0.226

Gnomad4 OTH exome

AF:

0.243

GnomAD4 genome

AF:

0.247

AC:

37611

AN:

152086

Hom.:

4915

Cov.:

AF XY:

0.248

AC XY:

18444

AN XY:

74344

show subpopulations

Gnomad4 AFR

AF:

0.257

Gnomad4 AMR

AF:

0.290

Gnomad4 ASJ

AF:

0.197

Gnomad4 EAS

AF:

0.413

Gnomad4 SAS

AF:

0.255

Gnomad4 FIN

AF:

0.240

Gnomad4 NFE

AF:

0.222

Gnomad4 OTH

AF:

0.252

Alfa

AF:

0.227

Hom.:

512

Bravo

AF:

0.254

Asia WGS

AF:

0.407

AC:

1414

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	May 13, 2021	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.79

CADD

Benign

DANN

Benign

0.65

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