rs1005645

Positions:

• chr17-76700678-T-C

Variant summary

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

The NM_198530.4(MXRA7):​c.342+9927A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.837 in 152,244 control chromosomes in the GnomAD database, including 54,247 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 0.84 (54247 hom., cov: 34)
• Consequence: MXRA7 NM_198530.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -7.03

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=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.919 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MXRA7	NM_198530.4	c.342+9927A>G		intron_variant		ENST00000449428.7
MXRA7	NM_001008528.3	c.342+9927A>G		intron_variant
MXRA7	NM_001008529.3	c.342+9927A>G		intron_variant
MXRA7	NR_130926.2	n.61+8820A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MXRA7	ENST00000449428.7	c.342+9927A>G		intron_variant		1	NM_198530.4	P2
MXRA7	ENST00000355797.7	c.342+9927A>G		intron_variant		2		A2
MXRA7	ENST00000375036.6	c.342+9927A>G		intron_variant		2		A2
MXRA7	ENST00000588114.5	c.-124+8820A>G		intron_variant		4		A2

Frequencies

GnomAD3 genomes AF: 0.837 AC: 127315 AN: 152126 Hom.: 54219 Cov.: 34

Gnomad AFR AF: 0.678

Gnomad AMI AF: 0.989

Gnomad AMR AF: 0.864

Gnomad ASJ AF: 0.915

Gnomad EAS AF: 0.697

Gnomad SAS AF: 0.836

Gnomad FIN AF: 0.878

Gnomad MID AF: 0.877

Gnomad NFE AF: 0.925

Gnomad OTH AF: 0.845

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.837 AC: 127399 AN: 152244 Hom.: 54247 Cov.: 34 AF XY: 0.835 AC XY: 62160 AN XY: 74432

Gnomad4 AFR AF: 0.678

Gnomad4 AMR AF: 0.864

Gnomad4 ASJ AF: 0.915

Gnomad4 EAS AF: 0.697

Gnomad4 SAS AF: 0.837

Gnomad4 FIN AF: 0.878

Gnomad4 NFE AF: 0.925

Gnomad4 OTH AF: 0.844

Alfa AF: 0.909 Hom.: 82045

Bravo AF: 0.827

Asia WGS AF: 0.753 AC: 2621 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.22
DANN	Benign	0.36

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: rs1005645; hg19: chr17-74696760; COSMIC: COSV63322057; COSMIC: COSV63322057;