Variant 9-36110066-T-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_ModerateBP6BP7BA1

The NM_021111.3(RECK):c.1875T>A(p.Arg625=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.351 in 1,606,556 control chromosomes in the GnomAD database, including 103,114 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in Lovd as Benign (no stars).

Frequency

Genomes: 𝑓 0.28 ( 7259 hom., cov: 32)

Exomes 𝑓: 0.36 ( 95855 hom. )

Consequence

RECK
NM_021111.3 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.918

Variant links:

Genes affected

RECK (HGNC:11345): (reversion inducing cysteine rich protein with kazal motifs) The protein encoded by this gene is a cysteine-rich, extracellular protein with protease inhibitor-like domains whose expression is suppressed strongly in many tumors and cells transformed by various kinds of oncogenes. In normal cells, this membrane-anchored glycoprotein may serve as a negative regulator for matrix metalloproteinase-9, a key enzyme involved in tumor invasion and metastasis. Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Oct 2015]

RECK links:

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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=-0.45).

BP6

Variant 9-36110066-T-A is Benign according to our data. Variant chr9-36110066-T-A is described in Lovd as [Benign].

BP7

Synonymous conserved (PhyloP=-0.918 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.372 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein
RECK	NM_021111.3 linkuse as main transcript	c.1875T>A	p.Arg625=	synonymous_variant	15/21	ENST00000377966.4	NP_066934.1
RECK	NM_001316345.2 linkuse as main transcript	c.1491T>A	p.Arg497=	synonymous_variant	17/23		NP_001303274.1
RECK	XM_017015207.2 linkuse as main transcript	c.1764T>A	p.Arg588=	synonymous_variant	16/22		XP_016870696.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RECK	ENST00000377966.4 linkuse as main transcript	c.1875T>A	p.Arg625=	synonymous_variant	15/21	1	NM_021111.3	ENSP00000367202	P1

Frequencies

GnomAD3 genomes

AF:

0.281

AC:

42751

AN:

152018

Hom.:

7261

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0923

Gnomad AMI

AF:

0.241

Gnomad AMR

AF:

0.271

Gnomad ASJ

AF:

0.446

Gnomad EAS

AF:

0.260

Gnomad SAS

AF:

0.352

Gnomad FIN

AF:

0.342

Gnomad MID

AF:

0.453

Gnomad NFE

AF:

0.376

Gnomad OTH

AF:

0.322

GnomAD3 exomes

AF:

0.323

AC:

81055

AN:

251228

Hom.:

14212

AF XY:

0.335

AC XY:

45451

AN XY:

135766

show subpopulations

Gnomad AFR exome

AF:

0.0835

Gnomad AMR exome

AF:

0.218

Gnomad ASJ exome

AF:

0.451

Gnomad EAS exome

AF:

0.254

Gnomad SAS exome

AF:

0.354

Gnomad FIN exome

AF:

0.341

Gnomad NFE exome

AF:

0.375

Gnomad OTH exome

AF:

0.345

GnomAD4 exome

AF:

0.358

AC:

520514

AN:

1454420

Hom.:

95855

Cov.:

AF XY:

0.360

AC XY:

259789

AN XY:

721896

show subpopulations

Gnomad4 AFR exome

AF:

0.0810

Gnomad4 AMR exome

AF:

0.225

Gnomad4 ASJ exome

AF:

0.450

Gnomad4 EAS exome

AF:

0.269

Gnomad4 SAS exome

AF:

0.358

Gnomad4 FIN exome

AF:

0.348

Gnomad4 NFE exome

AF:

0.373

Gnomad4 OTH exome

AF:

0.355

GnomAD4 genome

AF:

0.281

AC:

42738

AN:

152136

Hom.:

7259

Cov.:

AF XY:

0.283

AC XY:

21019

AN XY:

74368

show subpopulations

Gnomad4 AFR

AF:

0.0921

Gnomad4 AMR

AF:

0.270

Gnomad4 ASJ

AF:

0.446

Gnomad4 EAS

AF:

0.261

Gnomad4 SAS

AF:

0.351

Gnomad4 FIN

AF:

0.342

Gnomad4 NFE

AF:

0.376

Gnomad4 OTH

AF:

0.319

Alfa

AF:

0.358

Hom.:

3403

Bravo

AF:

0.264

Asia WGS

AF:

0.281

AC:

981

AN:

3478

EpiCase

AF:

0.389

EpiControl

AF:

0.382

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.45

CADD

Benign

5.3

DANN

Benign

0.63

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over