15-71826436-G-C

Variant names:

• chr15-71826436-G-C
• rs2625529
• NM_006901.4:c.*144C>G

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

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
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: 3.63

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]

ACMG classification

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 rank	MANE	Protein	UniProt
MYO9A	NM_006901.4	c.*144C>G		3_prime_UTR_variant	Exon 42 of 42	ENST00000356056.10	NP_008832.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MYO9A	ENST00000356056	c.*144C>G		3_prime_UTR_variant	Exon 42 of 42	1	NM_006901.4	ENSP00000348349.5
MYO9A	ENST00000564571	c.*596C>G		3_prime_UTR_variant	Exon 42 of 42	1		ENSP00000456192.1
MYO9A	ENST00000561618	c.*144C>G		3_prime_UTR_variant	Exon 19 of 19	1		ENSP00000457945.1
MYO9A	ENST00000568042	c.*144C>G		3_prime_UTR_variant	Exon 9 of 9	5		ENSP00000457407.1

Frequencies

GnomAD3 genomes AF: 0.247 AC: 37574 AN: 151968 Hom.: 4906 Cov.: 32

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.: 8 AF XY: 0.237 AC XY: 74045 AN XY: 312806

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.: 32 AF XY: 0.248 AC XY: 18444 AN XY: 74344

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

Submissions by phenotype

not provided Benign:2

May 13, 2021

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	15
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

Other links and lift over

dbSNP: rs2625529; hg19: chr15-72118777; COSMIC: COSV61850193; COSMIC: COSV61850193;