Variant chr2-111898815-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_006343.3(MERTK):c.61+19G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0432 in 1,577,290 control chromosomes in the GnomAD database, including 1,612 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.048 ( 159 hom., cov: 32)

Exomes 𝑓: 0.043 ( 1453 hom. )

Consequence

MERTK
NM_006343.3 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:4

Conservation

PhyloP100: -0.0750

Variant links:

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]

MERTK links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.77).

BP6

Variant 2-111898815-G-A is Benign according to our data. Variant chr2-111898815-G-A is described in ClinVar as [Benign]. Clinvar id is 287486.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0561 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MERTK	NM_006343.3 linkuse as main transcript	c.61+19G>A		intron_variant		ENST00000295408.9

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Appris
MERTK	ENST00000295408.9 linkuse as main transcript	c.61+19G>A	intron_variant	1	NM_006343.3	P1
MERTK	ENST00000439966.5 linkuse as main transcript	c.61+19G>A	intron_variant, NMD_transcript_variant	1
MERTK	ENST00000409780.5 linkuse as main transcript	c.-47+19G>A	intron_variant	5

Frequencies

GnomAD3 genomes

AF:

0.0476

AC:

7248

AN:

152144

Hom.:

159

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0580

Gnomad AMI

AF:

0.0593

Gnomad AMR

AF:

0.0375

Gnomad ASJ

AF:

0.0297

Gnomad EAS

AF:

0.00270

Gnomad SAS

AF:

0.0209

Gnomad FIN

AF:

0.0665

Gnomad MID

AF:

0.0285

Gnomad NFE

AF:

0.0467

Gnomad OTH

AF:

0.0521

GnomAD3 exomes

AF:

0.0396

AC:

6981

AN:

176206

Hom.:

181

AF XY:

0.0388

AC XY:

3751

AN XY:

96774

show subpopulations

Gnomad AFR exome

AF:

0.0612

Gnomad AMR exome

AF:

0.0327

Gnomad ASJ exome

AF:

0.0332

Gnomad EAS exome

AF:

0.00170

Gnomad SAS exome

AF:

0.0216

Gnomad FIN exome

AF:

0.0693

Gnomad NFE exome

AF:

0.0469

Gnomad OTH exome

AF:

0.0437

GnomAD4 exome

AF:

0.0427

AC:

60883

AN:

1425028

Hom.:

1453

Cov.:

AF XY:

0.0421

AC XY:

29680

AN XY:

705374

show subpopulations

Gnomad4 AFR exome

AF:

0.0561

Gnomad4 AMR exome

AF:

0.0334

Gnomad4 ASJ exome

AF:

0.0359

Gnomad4 EAS exome

AF:

0.00215

Gnomad4 SAS exome

AF:

0.0232

Gnomad4 FIN exome

AF:

0.0688

Gnomad4 NFE exome

AF:

0.0449

Gnomad4 OTH exome

AF:

0.0387

GnomAD4 genome

AF:

0.0477

AC:

7257

AN:

152262

Hom.:

159

Cov.:

AF XY:

0.0479

AC XY:

3566

AN XY:

74446

show subpopulations

Gnomad4 AFR

AF:

0.0580

Gnomad4 AMR

AF:

0.0376

Gnomad4 ASJ

AF:

0.0297

Gnomad4 EAS

AF:

0.00271

Gnomad4 SAS

AF:

0.0207

Gnomad4 FIN

AF:

0.0665

Gnomad4 NFE

AF:

0.0467

Gnomad4 OTH

AF:

0.0511

Alfa

AF:

0.0326

Hom.:

Bravo

AF:

0.0453

Asia WGS

AF:

0.0200

AC:

AN:

3476

ClinVar

Significance: Benign

Submissions summary: Benign:4

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 30, 2024	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

Eurofins Ntd Llc (ga)

Apr 13, 2016

- -

Retinitis pigmentosa 38

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Sep 05, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.77

CADD

Benign

7.3

DANN

Benign

0.87

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.3

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over