chr17-76700678-T-C

Variant names:

• chr17-76700678-T-C
• rs1005645
• NM_198530.4:c.342+9927A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001008528.3(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_001008528.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -7.03
• Publications: 11 publications found

Genes affected

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

ENSG00000296346 (HGNC:):

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001008528.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MXRA7	NM_198530.4	MANE Select	c.342+9927A>G		intron	N/A	NP_940932.2
	MXRA7	NM_001008528.3		c.342+9927A>G		intron	N/A	NP_001008528.1
	MXRA7	NM_001008529.3		c.342+9927A>G		intron	N/A	NP_001008529.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MXRA7	ENST00000449428.7	TSL:1 MANE Select	c.342+9927A>G		intron	N/A	ENSP00000391466.1
	MXRA7	ENST00000355797.7	TSL:2	c.342+9927A>G		intron	N/A	ENSP00000348050.2
	MXRA7	ENST00000375036.6	TSL:2	c.342+9927A>G		intron	N/A	ENSP00000364176.1

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

African (AFR) AF: 0.678 AC: 28170 AN: 41544

American (AMR) AF: 0.864 AC: 13217 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.915 AC: 3178 AN: 3472

East Asian (EAS) AF: 0.697 AC: 3594 AN: 5156

South Asian (SAS) AF: 0.837 AC: 4046 AN: 4834

European-Finnish (FIN) AF: 0.878 AC: 9302 AN: 10596

Middle Eastern (MID) AF: 0.871 AC: 256 AN: 294

European-Non Finnish (NFE) AF: 0.925 AC: 62951 AN: 68030

Other (OTH) AF: 0.844 AC: 1783 AN: 2112

Alfa AF: 0.897 Hom.: 111787

Bravo AF: 0.827

Asia WGS AF: 0.753 AC: 2621 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.22
DANN	Benign	0.36
PhyloP100		-7.0
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

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