17-76710881-G-A

Variant names:

• chr17-76710881-G-A
• rs1024112369
• NM_198530.4:c.66C>T

Variant summary

Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_Strong BP6_Moderate BP7

The NM_198530.4(MXRA7):​c.66C>T​(p.Leu22Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000232 in 146,374 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.00023 (0 hom., cov: 29)
  • Exomes 𝑓: 0.00030 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: MXRA7 NM_198530.4 synonymous
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.53

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -7 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.5).
• BP6: Variant 17-76710881-G-A is Benign according to our data. Variant chr17-76710881-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 3778193.Status of the report is criteria_provided_single_submitter, 1 stars.
• BP7: Synonymous conserved (PhyloP=-1.53 with no splicing effect.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MXRA7	NM_198530.4	c.66C>T	p.Leu22Leu	synonymous_variant	Exon 1 of 4	ENST00000449428.7	NP_940932.2
MXRA7	NM_001008528.3	c.66C>T	p.Leu22Leu	synonymous_variant	Exon 1 of 4		NP_001008528.1
MXRA7	NM_001008529.3	c.66C>T	p.Leu22Leu	synonymous_variant	Exon 1 of 5		NP_001008529.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MXRA7	ENST00000449428.7	c.66C>T	p.Leu22Leu	synonymous_variant	Exon 1 of 4	1	NM_198530.4	ENSP00000391466.1
MXRA7	ENST00000355797.7	c.66C>T	p.Leu22Leu	synonymous_variant	Exon 1 of 4	2		ENSP00000348050.2
MXRA7	ENST00000375036.6	c.66C>T	p.Leu22Leu	synonymous_variant	Exon 1 of 5	2		ENSP00000364176.1

Frequencies

GnomAD3 genomes AF: 0.000219 AC: 32 AN: 146266 Hom.: 0 Cov.: 29

Gnomad AFR AF: 0.0000735

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0000678

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00321

Gnomad NFE AF: 0.000410

Gnomad OTH AF: 0.00

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.000303 AC: 257 AN: 848262 Hom.: 0 Cov.: 23 AF XY: 0.000306 AC XY: 121 AN XY: 396034

Gnomad4 AFR exome AF: 0.0000633

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.000325

Gnomad4 OTH exome AF: 0.000180

GnomAD4 genome AF: 0.000232 AC: 34 AN: 146374 Hom.: 0 Cov.: 29 AF XY: 0.000154 AC XY: 11 AN XY: 71270

Gnomad4 AFR AF: 0.000122

Gnomad4 AMR AF: 0.0000677

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000410

Gnomad4 OTH AF: 0.00

Alfa AF: 0.000169 Hom.: 0

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Mar 01, 2025

CeGaT Center for Human Genetics Tuebingen

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

MXRA7: BP4, BP7 -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.50
CADD	Benign	9.4
DANN	Uncertain	0.98

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

Other links and lift over

dbSNP: rs1024112369; hg19: chr17-74706963;