2-69924339-A-T

Variant names:

• chr2-69924339-A-T
• rs10205487
• NM_002357.4:c.203+2574A>T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_002357.4(MXD1):​c.203+2574A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 33)
• Consequence: MXD1 NM_002357.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.370
• Publications: 9 publications found

Genes affected

MXD1 (HGNC:6761): (MAX dimerization protein 1) This gene encodes a member of the MYC/MAX/MAD network of basic helix-loop-helix leucine zipper transcription factors. The MYC/MAX/MAD transcription factors mediate cellular proliferation, differentiation and apoptosis. The encoded protein antagonizes MYC-mediated transcriptional activation of target genes by competing for the binding partner MAX and recruiting repressor complexes containing histone deacetylases. Mutations in this gene may play a role in acute leukemia, and the encoded protein is a potential tumor suppressor. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Feb 2011]

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MXD1	NM_002357.4	c.203+2574A>T		intron_variant	Intron 3 of 5	ENST00000264444.7	NP_002348.1
MXD1	NM_001202513.2	c.203+2574A>T		intron_variant	Intron 3 of 5		NP_001189442.1
MXD1	NM_001202514.2	c.173+8119A>T		intron_variant	Intron 2 of 4		NP_001189443.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MXD1	ENST00000264444.7	c.203+2574A>T		intron_variant	Intron 3 of 5	1	NM_002357.4	ENSP00000264444.2
MXD1	ENST00000540449.5	c.173+8119A>T		intron_variant	Intron 2 of 4	1		ENSP00000443935.1
MXD1	ENST00000435990.5	c.107+2574A>T		intron_variant	Intron 5 of 7	3		ENSP00000410672.1
MXD1	ENST00000409442.2	n.77+8119A>T		intron_variant	Intron 2 of 4	2		ENSP00000386523.2

Frequencies

GnomAD3 genomes Cov.: 33

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

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	1.6
DANN	Benign	0.43
PhyloP100		-0.37

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: rs10205487; hg19: chr2-70151471;