rs2893363

Positions:

• chr7-30139438-A-G
• chr7-30139438-A-T

Variant summary

Our verdict is Benign. Variant got -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

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 Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MTURN	NM_152793.3	c.162+4140A>G		intron_variant		ENST00000324453.13
MTURN	XM_005249652.4	c.162+4140A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MTURN	ENST00000324453.13	c.162+4140A>G		intron_variant		1	NM_152793.3	P1
MTURN	ENST00000409688.1	c.162+4140A>G		intron_variant		2
MTURN	ENST00000434060.1	c.111+1744A>G		intron_variant		2

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

Gnomad4 AFR AF: 0.552

Gnomad4 AMR AF: 0.764

Gnomad4 ASJ AF: 0.824

Gnomad4 EAS AF: 0.938

Gnomad4 SAS AF: 0.795

Gnomad4 FIN AF: 0.817

Gnomad4 NFE AF: 0.791

Gnomad4 OTH AF: 0.741

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.041
DANN	Benign	0.65

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;