Genetic Variant ENST00000592148.1:c.291C>T (chr17-76688357-G-A) – ACMG Classification: Benign (-11 pts)

Variant summary

Our verdict is Benign. The variant received -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2

The ENST00000592148.1(MXRA7):c.291C>T(p.Gly97Gly) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00189 in 1,438,692 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0017 ( 0 hom., cov: 33)

Exomes 𝑓: 0.0019 ( 3 hom. )

Consequence

MXRA7
ENST00000592148.1 synonymous

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.0910

Publications

0 publications found

Variant links:

Genes affected

MXRA7 (HGNC:7541): (matrix remodeling associated 7) Located in endoplasmic reticulum. [provided by Alliance of Genome Resources, Apr 2022]

MXRA7 links:

SNHG16 (HGNC:44352): (small nucleolar RNA host gene 16)

SNHG16 links:

ENSG00000296346 (HGNC:):

ENSG00000296346 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -11 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.92).

BP6

Variant 17-76688357-G-A is Benign according to our data. Variant chr17-76688357-G-A is described in ClinVar as Likely_benign. ClinVar VariationId is 2648318.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=-0.091 with no splicing effect.

BS2

High Homozygotes in GnomAdExome4 at 3 AR gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000592148.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein
MXRA7	NM_198530.4	MANE Select	c.343-181C>T		intron	N/A	NP_940932.2
MXRA7	NM_001387276.1		c.291C>T	p.Gly97Gly	synonymous	Exon 1 of 3	NP_001374205.1
MXRA7	NM_001387277.1		c.291C>T	p.Gly97Gly	synonymous	Exon 1 of 4	NP_001374206.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
MXRA7	ENST00000592148.1	TSL:1	c.291C>T	p.Gly97Gly	synonymous	Exon 1 of 3	ENSP00000465103.1	Q6ZR64
MXRA7	ENST00000449428.7	TSL:1 MANE Select	c.343-181C>T		intron	N/A	ENSP00000391466.1	P84157-2
MXRA7	ENST00000355797.7	TSL:2	c.343-181C>T		intron	N/A	ENSP00000348050.2	P84157-1

Frequencies

GnomAD3 genomes

AF:

0.00166

AC:

253

AN:

152238

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000314

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00517

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00160

Gnomad MID

AF:

0.00316

Gnomad NFE

AF:

0.00209

Gnomad OTH

AF:

0.000478

GnomAD2 exomes

AF:

0.00166

AC:

112

AN:

67414

AF XY:

0.00172

show subpopulations

Gnomad AFR exome

AF:

0.000157

Gnomad AMR exome

AF:

0.00345

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.000868

Gnomad NFE exome

AF:

0.00238

Gnomad OTH exome

AF:

0.000944

GnomAD4 exome

AF:

0.00191

AC:

2460

AN:

1286336

Hom.:

Cov.:

AF XY:

0.00181

AC XY:

1130

AN XY:

624182

show subpopulations

African (AFR)

AF:

0.000353

AC:

AN:

28316

American (AMR)

AF:

0.00204

AC:

AN:

20548

Ashkenazi Jewish (ASJ)

AF:

0.000369

AC:

AN:

18948

East Asian (EAS)

AF:

0.00

AC:

AN:

34374

South Asian (SAS)

AF:

0.00

AC:

AN:

63060

European-Finnish (FIN)

AF:

0.00129

AC:

AN:

30942

Middle Eastern (MID)

AF:

0.000191

AC:

AN:

5240

European-Non Finnish (NFE)

AF:

0.00222

AC:

2292

AN:

1031232

Other (OTH)

AF:

0.00127

AC:

AN:

53676

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.489

Heterozygous variant carriers

149

298

446

595

744

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

180

270

360

450

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.00166

AC:

253

AN:

152356

Hom.:

Cov.:

AF XY:

0.00165

AC XY:

123

AN XY:

74508

show subpopulations

African (AFR)

AF:

0.000313

AC:

AN:

41580

American (AMR)

AF:

0.00516

AC:

AN:

15308

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

3472

East Asian (EAS)

AF:

0.00

AC:

AN:

5182

South Asian (SAS)

AF:

0.00

AC:

AN:

4834

European-Finnish (FIN)

AF:

0.00160

AC:

AN:

10630

Middle Eastern (MID)

AF:

0.00340

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.00209

AC:

142

AN:

68030

Other (OTH)

AF:

0.000473

AC:

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.498

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.00244

Hom.:

Bravo

AF:

0.00151

ClinVar

ClinVar submissions

Significance:Likely benign

Revision:criteria provided, single submitter

View on ClinVar

Pathogenic

VUS

Benign

Condition

not provided (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

2.0

(source)

DANN

Benign

0.78

PhyloP100

-0.091

PromoterAI

-0.027

Neutral

(source)

Mutation Taster

=100/0

polymorphism

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.040

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over