17-76676325-G-T

Position:

• chr17-76676325-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001387276.1(MXRA7):​c.*1263C>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.184 in 152,128 control chromosomes in the GnomAD database, including 3,279 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.18 (3278 hom., cov: 33)
  • Exomes 𝑓: 0.50 (1 hom.)
• Consequence: MXRA7 NM_001387276.1 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.500

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.506 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MXRA7	NM_001008528.3	c.*1263C>A		3_prime_UTR_variant	4/4		NP_001008528.1
MXRA7	NM_001387276.1	c.*1263C>A		3_prime_UTR_variant	3/3		NP_001374205.1
MXRA7	NM_001387278.1	c.*1263C>A		3_prime_UTR_variant	4/4		NP_001374207.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MXRA7	ENST00000355797.7	c.*1263C>A		3_prime_UTR_variant	4/4	2		ENSP00000348050	A2

Frequencies

GnomAD3 genomes AF: 0.184 AC: 27945 AN: 152002 Hom.: 3282 Cov.: 33

Gnomad AFR AF: 0.254

Gnomad AMI AF: 0.0154

Gnomad AMR AF: 0.233

Gnomad ASJ AF: 0.117

Gnomad EAS AF: 0.522

Gnomad SAS AF: 0.230

Gnomad FIN AF: 0.141

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.113

Gnomad OTH AF: 0.192

GnomAD4 exome AF: 0.500 AC: 4 AN: 8 Hom.: 1 Cov.: 0 AF XY: 0.500 AC XY: 4 AN XY: 8

Gnomad4 FIN exome AF: 0.500

Gnomad4 NFE exome AF: 0.500

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.184 AC: 27946 AN: 152120 Hom.: 3278 Cov.: 33 AF XY: 0.189 AC XY: 14024 AN XY: 74352

Gnomad4 AFR AF: 0.254

Gnomad4 AMR AF: 0.233

Gnomad4 ASJ AF: 0.117

Gnomad4 EAS AF: 0.522

Gnomad4 SAS AF: 0.230

Gnomad4 FIN AF: 0.141

Gnomad4 NFE AF: 0.113

Gnomad4 OTH AF: 0.191

Alfa AF: 0.137 Hom.: 400

Bravo AF: 0.196

Asia WGS AF: 0.356 AC: 1236 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.10
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

Other links and lift over

dbSNP: rs10473; hg19: chr17-74672407;