rs1516640

Positions:

• chr2-111917281-G-A
• chr2-111917281-G-C
• chr2-111917281-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_006343.3(MERTK):​c.62-11839G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.464 in 151,928 control chromosomes in the GnomAD database, including 16,520 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 0.46 (16520 hom., cov: 31)
• Consequence: MERTK NM_006343.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.19

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.717 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MERTK	NM_006343.3	c.62-11839G>A		intron_variant		ENST00000295408.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MERTK	ENST00000295408.9	c.62-11839G>A		intron_variant		1	NM_006343.3	P1
MERTK	ENST00000439966.5	c.62-11839G>A		intron_variant, NMD_transcript_variant		1
MERTK	ENST00000409780.5	c.-47+18485G>A		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.464 AC: 70448 AN: 151810 Hom.: 16504 Cov.: 31

Gnomad AFR AF: 0.440

Gnomad AMI AF: 0.668

Gnomad AMR AF: 0.460

Gnomad ASJ AF: 0.478

Gnomad EAS AF: 0.736

Gnomad SAS AF: 0.441

Gnomad FIN AF: 0.414

Gnomad MID AF: 0.443

Gnomad NFE AF: 0.465

Gnomad OTH AF: 0.473

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.464 AC: 70506 AN: 151928 Hom.: 16520 Cov.: 31 AF XY: 0.462 AC XY: 34288 AN XY: 74232

Gnomad4 AFR AF: 0.440

Gnomad4 AMR AF: 0.460

Gnomad4 ASJ AF: 0.478

Gnomad4 EAS AF: 0.737

Gnomad4 SAS AF: 0.441

Gnomad4 FIN AF: 0.414

Gnomad4 NFE AF: 0.465

Gnomad4 OTH AF: 0.471

Alfa AF: 0.461 Hom.: 8531

Bravo AF: 0.471

Asia WGS AF: 0.555 AC: 1928 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.72
DANN	Benign	0.73

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: rs1516640; hg19: chr2-112674858; COSMIC: COSV54926437;