6-10763546-TA-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_001242957.3(MAK):c.*905del variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.82 (46547 hom., cov: 0)
  • Exomes 𝑓: 0.50 (0 hom.)
• Consequence: MAK NM_001242957.3 3_prime_UTR
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.973

Genes affected

MAK (HGNC:6816): (male germ cell associated kinase) The product of this gene is a serine/threonine protein kinase related to kinases involved in cell cycle regulation. Studies of the mouse and rat homologs have localized the kinase to the chromosomes during meiosis in spermatogenesis, specifically to the synaptonemal complex that exists while homologous chromosomes are paired. Mutations in this gene have been associated with ciliary defects resulting in retinitis pigmentosa 62. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2016]

TMEM14B (HGNC:21384): (transmembrane protein 14B) Enables identical protein binding activity. Involved in cerebral cortex development; neural precursor cell proliferation; and regulation of G1/S transition of mitotic cell cycle. Predicted to be integral component of membrane. Predicted to be active in mitochondrial inner membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 6-10763546-TA-T is Benign according to our data. Variant chr6-10763546-TA-T is described in ClinVar as [Benign]. Clinvar id is 354775.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.903 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MAK	NM_001242957.3	c.*905del		3_prime_UTR_variant	15/15	ENST00000354489.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MAK	ENST00000354489.7	c.*905del		3_prime_UTR_variant	15/15	5	NM_001242957.3	P4

Frequencies

GnomAD3 genomes AF: 0.819 AC: 114180 AN: 139430 Hom.: 46544 Cov.: 0

Gnomad AFR AF: 0.912

Gnomad AMI AF: 0.768

Gnomad AMR AF: 0.774

Gnomad ASJ AF: 0.707

Gnomad EAS AF: 0.916

Gnomad SAS AF: 0.803

Gnomad FIN AF: 0.832

Gnomad MID AF: 0.752

Gnomad NFE AF: 0.775

Gnomad OTH AF: 0.787

GnomAD4 exome AF: 0.500 AC: 1 AN: 2 Hom.: 0 Cov.: 0 AF XY: 0.500 AC XY: 1 AN XY: 2

Gnomad4 NFE exome AF: 0.500

GnomAD4 genome AF: 0.819 AC: 114205 AN: 139466 Hom.: 46547 Cov.: 0 AF XY: 0.819 AC XY: 55056 AN XY: 67186

Gnomad4 AFR AF: 0.911

Gnomad4 AMR AF: 0.774

Gnomad4 ASJ AF: 0.707

Gnomad4 EAS AF: 0.915

Gnomad4 SAS AF: 0.802

Gnomad4 FIN AF: 0.832

Gnomad4 NFE AF: 0.775

Gnomad4 OTH AF: 0.786

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

Retinitis Pigmentosa, Recessive Benign:1

Benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jun 14, 2016

- -

Computational scores

Source: dbNSFP v4.3

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: rs35696238; hg19: chr6-10763779;