rs869016
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_006343.3(MERTK):c.61+2737G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.356 in 150,528 control chromosomes in the GnomAD database, including 9,955 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.36 ( 9955 hom., cov: 29)
Consequence
MERTK
NM_006343.3 intron
NM_006343.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.00900
Genes affected
MERTK (HGNC:7027): (MER proto-oncogene, tyrosine kinase) This gene is a member of the MER/AXL/TYRO3 receptor kinase family and encodes a transmembrane protein with two fibronectin type-III domains, two Ig-like C2-type (immunoglobulin-like) domains, and one tyrosine kinase domain. Mutations in this gene have been associated with disruption of the retinal pigment epithelium (RPE) phagocytosis pathway and onset of autosomal recessive retinitis pigmentosa (RP). [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.88).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.713 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MERTK | NM_006343.3 | c.61+2737G>A | intron_variant | ENST00000295408.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MERTK | ENST00000295408.9 | c.61+2737G>A | intron_variant | 1 | NM_006343.3 | P1 | |||
MERTK | ENST00000439966.5 | c.61+2737G>A | intron_variant, NMD_transcript_variant | 1 | |||||
MERTK | ENST00000409780.5 | c.-47+2737G>A | intron_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.355 AC: 53467AN: 150426Hom.: 9943 Cov.: 29
GnomAD3 genomes
?
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150426
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29
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.356 AC: 53515AN: 150528Hom.: 9955 Cov.: 29 AF XY: 0.356 AC XY: 26150AN XY: 73390
GnomAD4 genome
?
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AC:
53515
AN:
150528
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29
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26150
AN XY:
73390
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1799
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3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at