chr7-30139438-A-G

Variant names:

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

Variant summary

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

The NM_152793.3(MTURN):​c.162+4140A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.73 in 152,122 control chromosomes in the GnomAD database, including 41,501 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 0.73 (41501 hom., cov: 32)
• Consequence: MTURN NM_152793.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.65
• Publications: 2 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.916 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_152793.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MTURN	NM_152793.3	MANE Select	c.162+4140A>G		intron	N/A	NP_690006.2	Q8N3F0-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MTURN	ENST00000324453.13	TSL:1 MANE Select	c.162+4140A>G		intron	N/A	ENSP00000324204.8	Q8N3F0-1
	MTURN	ENST00000409688.1	TSL:2	c.162+4140A>G		intron	N/A	ENSP00000386490.1	Q8N3F0-4
	MTURN	ENST00000434060.1	TSL:2	c.111+1744A>G		intron	N/A	ENSP00000415658.1	C9JBT1

Frequencies

GnomAD3 genomes AF: 0.730 AC: 110957 AN: 152004 Hom.: 41498 Cov.: 32

Gnomad AFR AF: 0.552

Gnomad AMI AF: 0.709

Gnomad AMR AF: 0.764

Gnomad ASJ AF: 0.824

Gnomad EAS AF: 0.938

Gnomad SAS AF: 0.794

Gnomad FIN AF: 0.817

Gnomad MID AF: 0.725

Gnomad NFE AF: 0.791

Gnomad OTH AF: 0.740

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

GnomAD4 genome AF: 0.730 AC: 110998 AN: 152122 Hom.: 41501 Cov.: 32 AF XY: 0.732 AC XY: 54417 AN XY: 74372

African (AFR) AF: 0.552 AC: 22887 AN: 41468

American (AMR) AF: 0.764 AC: 11679 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.824 AC: 2861 AN: 3472

East Asian (EAS) AF: 0.938 AC: 4856 AN: 5178

South Asian (SAS) AF: 0.795 AC: 3833 AN: 4824

European-Finnish (FIN) AF: 0.817 AC: 8651 AN: 10586

Middle Eastern (MID) AF: 0.704 AC: 207 AN: 294

European-Non Finnish (NFE) AF: 0.791 AC: 53819 AN: 68006

Other (OTH) AF: 0.741 AC: 1558 AN: 2102

Alfa AF: 0.752 Hom.: 5148

Bravo AF: 0.719

Asia WGS AF: 0.852 AC: 2962 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.041
DANN	Benign	0.65
PhyloP100		-1.6
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: rs2893363; hg19: chr7-30179054;