NM_152793.3:c.162+4140A>T

Variant names:

• chr7-30139438-A-T
• rs2893363
• NM_152793.3:c.162+4140A>T

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_152793.3(MTURN):​c.162+4140A>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: 32)
• Consequence: MTURN NM_152793.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.65

Genes affected

MTURN (HGNC:25457): (maturin, neural progenitor differentiation regulator homolog) Involved in negative regulation of NF-kappaB transcription factor activity; positive regulation of MAPK cascade; and positive regulation of megakaryocyte differentiation. Located in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MTURN	NM_152793.3	c.162+4140A>T		intron_variant	Intron 1 of 2	ENST00000324453.13	NP_690006.2
MTURN	XM_005249652.4	c.162+4140A>T		intron_variant	Intron 1 of 3		XP_005249709.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MTURN	ENST00000324453.13	c.162+4140A>T		intron_variant	Intron 1 of 2	1	NM_152793.3	ENSP00000324204.8
MTURN	ENST00000409688.1	c.162+4140A>T		intron_variant	Intron 1 of 1	2		ENSP00000386490.1
MTURN	ENST00000434060.1	c.111+1744A>T		intron_variant	Intron 1 of 1	2		ENSP00000415658.1

Frequencies

GnomAD3 genomes Cov.: 32

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

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.034
DANN	Benign	0.56

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: rs2893363; hg19: chr7-30179054;