Variant 17-76710715-C-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_198530.4(MXRA7):c.232G>T(p.Ala78Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000115 in 1,040,900 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 30)

Exomes 𝑓: 0.000012 ( 0 hom. )

Consequence

MXRA7
NM_198530.4 missense

Scores

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 0.736

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:

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (MetaRNN=0.057311773).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein
MXRA7	NM_198530.4 linkuse as main transcript	c.232G>T	p.Ala78Ser	missense_variant	1/4	ENST00000449428.7	NP_940932.2
MXRA7	NM_001008528.3 linkuse as main transcript	c.232G>T	p.Ala78Ser	missense_variant	1/4		NP_001008528.1
MXRA7	NM_001008529.3 linkuse as main transcript	c.232G>T	p.Ala78Ser	missense_variant	1/5		NP_001008529.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MXRA7	ENST00000449428.7 linkuse as main transcript	c.232G>T	p.Ala78Ser	missense_variant	1/4	1	NM_198530.4	ENSP00000391466	P2	P84157-2
MXRA7	ENST00000355797.7 linkuse as main transcript	c.232G>T	p.Ala78Ser	missense_variant	1/4	2		ENSP00000348050	A2	P84157-1
MXRA7	ENST00000375036.6 linkuse as main transcript	c.232G>T	p.Ala78Ser	missense_variant	1/5	2		ENSP00000364176	A2	P84157-3

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

AF:

0.0000115

AC:

AN:

1040900

Hom.:

Cov.:

AF XY:

0.0000101

AC XY:

AN XY:

496744

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 AMR exome

AF:

0.00

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.000529

Gnomad4 SAS exome

AF:

0.00

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.00

Gnomad4 OTH exome

AF:

0.00

GnomAD4 genome

Cov.:

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not specified

Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Ambry Genetics

Mar 29, 2022

The c.232G>T (p.A78S) alteration is located in exon 1 (coding exon 1) of the MXRA7 gene. This alteration results from a G to T substitution at nucleotide position 232, causing the alanine (A) at amino acid position 78 to be replaced by a serine (S). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.091

BayesDel_addAF

Benign

-0.24

BayesDel_noAF

Benign

-0.58

CADD

Benign

DANN

Benign

0.92

DEOGEN2

Benign

0.0018

T;.;.

Eigen

Benign

-1.0

Eigen_PC

Benign

-1.1

FATHMM_MKL

Benign

0.032

LIST_S2

Benign

0.45

T;T;T

M_CAP

Benign

0.015

MetaRNN

Benign

0.057

T;T;T

MetaSVM

Benign

-1.0

MutationAssessor

Benign

0.55

N;N;N

MutationTaster

Benign

1.0

N;N;N

PrimateAI

Uncertain

0.68

PROVEAN

Benign

-0.24

N;N;N

REVEL

Benign

0.021

Sift

Benign

0.97

T;T;T

Sift4G

Benign

0.44

T;T;T

Polyphen

0.61

P;P;P

Vest4

0.037

MutPred

0.28

Gain of glycosylation at A78 (P = 7e-04);Gain of glycosylation at A78 (P = 7e-04);Gain of glycosylation at A78 (P = 7e-04);

MVP

0.048

MPC

0.092

ClinPred

0.14

GERP RS

1.1

Varity_R

0.031

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