rs6730521

chr2-112026380-A-G

Variant summary

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

The NM_006343.3(MERTK):c.2487-1971A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.234 in 152,144 control chromosomes in the GnomAD database, including 4,493 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 0.23 (4493 hom., cov: 32)
• Consequence: MERTK NM_006343.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.717

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=-0.67).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.304 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MERTK	NM_006343.3	c.2487-1971A>G		intron_variant		ENST00000295408.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MERTK	ENST00000295408.9	c.2487-1971A>G		intron_variant		1	NM_006343.3	P1
MERTK	ENST00000439966.5	c.*1960-1971A>G		intron_variant, NMD_transcript_variant		1
MERTK	ENST00000409780.5	c.1959-1971A>G		intron_variant		5
MERTK	ENST00000449344.2	c.459-1971A>G		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.234 AC: 35566 AN: 152026 Hom.: 4486 Cov.: 32

Gnomad AFR AF: 0.175

Gnomad AMI AF: 0.227

Gnomad AMR AF: 0.286

Gnomad ASJ AF: 0.225

Gnomad EAS AF: 0.107

Gnomad SAS AF: 0.317

Gnomad FIN AF: 0.385

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.240

Gnomad OTH AF: 0.199

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

GnomAD4 genome AF: 0.234 AC: 35593 AN: 152144 Hom.: 4493 Cov.: 32 AF XY: 0.241 AC XY: 17956 AN XY: 74400

Gnomad4 AFR AF: 0.175

Gnomad4 AMR AF: 0.286

Gnomad4 ASJ AF: 0.225

Gnomad4 EAS AF: 0.106

Gnomad4 SAS AF: 0.317

Gnomad4 FIN AF: 0.385

Gnomad4 NFE AF: 0.240

Gnomad4 OTH AF: 0.198

Alfa AF: 0.232 Hom.: 3718

Bravo AF: 0.223

Asia WGS AF: 0.204 AC: 710 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
Cadd	Benign	10
Dann	Benign	0.90

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: rs6730521; hg19: chr2-112783957;