rs3757251

Variant names:

• chr6-13790904-T-A
• NM_001031713.4:c.1025-40A>T

Your query was ambiguous. Multiple possible variants found:

• chr6-13790904-T-A
• chr6-13790904-T-C
• chr6-13790904-T-G

Variant summary

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

The NM_001031713.4(MCUR1):​c.1025-40A>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: 31)
• Consequence: MCUR1 NM_001031713.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.133

Genes affected

MCUR1 (HGNC:21097): (mitochondrial calcium uniporter regulator 1) Involved in calcium import into the mitochondrion and positive regulation of mitochondrial calcium ion concentration. Is integral component of mitochondrial inner membrane. [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=-0.78).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MCUR1	NM_001031713.4	c.1025-40A>T		intron_variant	Intron 8 of 8	ENST00000379170.9	NP_001026883.1
MCUR1	XM_047419249.1	c.1268-40A>T		intron_variant	Intron 8 of 8		XP_047275205.1
MCUR1	XM_011514802.2	c.1024+974A>T		intron_variant	Intron 8 of 8		XP_011513104.1
MCUR1	XR_007059329.1	n.1243+974A>T		intron_variant	Intron 8 of 8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MCUR1	ENST00000379170.9	c.1025-40A>T		intron_variant	Intron 8 of 8	1	NM_001031713.4	ENSP00000368468.3
MCUR1	ENST00000607303.1	c.340+974A>T		intron_variant	Intron 5 of 6	3		ENSP00000476106.1
MCUR1	ENST00000488770.1	n.*837-40A>T		intron_variant	Intron 9 of 9	2		ENSP00000476162.1

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome Cov.: 17

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	3.1
DANN	Benign	0.83

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr6-13791136;