Variant chr11-119346601-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_031433.4(MFRP):c.-88C>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.528 in 1,374,554 control chromosomes in the GnomAD database, including 193,737 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.50 ( 19730 hom., cov: 32)

Exomes 𝑓: 0.53 ( 174007 hom. )

Consequence

MFRP
NM_031433.4 5_prime_UTR

Scores

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:4

Conservation

PhyloP100: -0.252

Variant links:

Genes affected

MFRP (HGNC:18121): (membrane frizzled-related protein) This gene encodes a member of the frizzled-related protein family. The encoded protein plays an important role in eye development and mutations in this gene have been associated with nanophthalmos, posterior microphthalmia, retinitis pigmentosa, foveoschisis, and optic disc drusen. The protein is encoded by a bicistronic transcript which also encodes C1q and tumor necrosis factor related protein 5 (C1QTNF5). [provided by RefSeq, Jun 2013]

MFRP links:

C1QTNF5 (HGNC:):

C1QTNF5 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.87).

BP6

Variant 11-119346601-G-A is Benign according to our data. Variant chr11-119346601-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 302987.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-119346601-G-A is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.715 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MFRP	NM_031433.4 linkuse as main transcript	c.-88C>T		5_prime_UTR_variant	1/15	ENST00000619721.6	NP_113621.1
C1QTNF5	NM_015645.5 linkuse as main transcript	c.-2724C>T		5_prime_UTR_variant	1/15		NP_056460.1

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MFRP	ENST00000619721.6 linkuse as main transcript	c.-88C>T	5_prime_UTR_variant	1/15	1	NM_031433.4	ENSP00000481824	P1	Q9BY79-1
MFRP	ENST00000360167.4 linkuse as main transcript	c.-88C>T	5_prime_UTR_variant	1/10	2		ENSP00000353291		Q9BY79-2
MFRP	ENST00000526059.1 linkuse as main transcript	n.17C>T	non_coding_transcript_exon_variant	1/3	3
MFRP	ENST00000634542.1 linkuse as main transcript	c.-88C>T	5_prime_UTR_variant, NMD_transcript_variant	1/5	3		ENSP00000488979

Frequencies

GnomAD3 genomes

AF:

0.504

AC:

76536

AN:

151878

Hom.:

19709

Cov.:

show subpopulations

Gnomad AFR

AF:

0.431

Gnomad AMI

AF:

0.659

Gnomad AMR

AF:

0.511

Gnomad ASJ

AF:

0.544

Gnomad EAS

AF:

0.734

Gnomad SAS

AF:

0.647

Gnomad FIN

AF:

0.497

Gnomad MID

AF:

0.684

Gnomad NFE

AF:

0.514

Gnomad OTH

AF:

0.537

GnomAD4 exome

AF:

0.531

AC:

649581

AN:

1222558

Hom.:

174007

Cov.:

AF XY:

0.535

AC XY:

331155

AN XY:

618652

show subpopulations

Gnomad4 AFR exome

AF:

0.437

Gnomad4 AMR exome

AF:

0.537

Gnomad4 ASJ exome

AF:

0.531

Gnomad4 EAS exome

AF:

0.735

Gnomad4 SAS exome

AF:

0.636

Gnomad4 FIN exome

AF:

0.477

Gnomad4 NFE exome

AF:

0.518

Gnomad4 OTH exome

AF:

0.545

GnomAD4 genome

AF:

0.504

AC:

76600

AN:

151996

Hom.:

19730

Cov.:

AF XY:

0.510

AC XY:

37858

AN XY:

74282

show subpopulations

Gnomad4 AFR

AF:

0.432

Gnomad4 AMR

AF:

0.512

Gnomad4 ASJ

AF:

0.544

Gnomad4 EAS

AF:

0.734

Gnomad4 SAS

AF:

0.647

Gnomad4 FIN

AF:

0.497

Gnomad4 NFE

AF:

0.514

Gnomad4 OTH

AF:

0.538

Alfa

AF:

0.442

Hom.:

2824

Bravo

AF:

0.504

Asia WGS

AF:

0.678

AC:

2353

AN:

3478

ClinVar

Significance: Benign/Likely 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	GeneDx	Nov 12, 2018	- -
Likely benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Isolated microphthalmia 6

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jun 14, 2016

- -

Retinal degeneration

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jun 14, 2016

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

2.3

DANN

Benign

0.60

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