NM_001388067.1:c.1263-14929A>C

Variant names:

• chr14-37531976-A-C
• rs17768343
• NM_001388067.1:c.1263-14929A>C

Variant summary

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

The NM_001388067.1(MIPOL1):​c.1263-14929A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.482 in 151,820 control chromosomes in the GnomAD database, including 19,712 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 0.48 (19712 hom., cov: 30)
• Consequence: MIPOL1 NM_001388067.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.347
• Publications: 4 publications found

Genes affected

MIPOL1 (HGNC:21460): (mirror-image polydactyly 1) This gene encodes a coiled-coil domain-containing protein. The encoded protein may function as a tumor suppressor. A translocation that results in truncation of the protein encoded by this locus has been associated with mirror-image polydactyly, also known as Laurin-Sandrow Syndrome. Alternatively spliced transcript variants have been described. [provided by RefSeq, Sep 2010]

ENSG00000259087 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.678 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MIPOL1	NM_001388067.1	c.1263-14929A>C		intron_variant	Intron 12 of 12	ENST00000684589.1	NP_001374996.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MIPOL1	ENST00000684589.1	c.1263-14929A>C		intron_variant	Intron 12 of 12		NM_001388067.1	ENSP00000506738.1

Frequencies

GnomAD3 genomes AF: 0.482 AC: 73122 AN: 151702 Hom.: 19716 Cov.: 30

Gnomad AFR AF: 0.217

Gnomad AMI AF: 0.763

Gnomad AMR AF: 0.538

Gnomad ASJ AF: 0.559

Gnomad EAS AF: 0.698

Gnomad SAS AF: 0.559

Gnomad FIN AF: 0.611

Gnomad MID AF: 0.529

Gnomad NFE AF: 0.580

Gnomad OTH AF: 0.507

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

GnomAD4 genome AF: 0.482 AC: 73110 AN: 151820 Hom.: 19712 Cov.: 30 AF XY: 0.487 AC XY: 36148 AN XY: 74186

African (AFR) AF: 0.217 AC: 8976 AN: 41398

American (AMR) AF: 0.537 AC: 8182 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.559 AC: 1938 AN: 3468

East Asian (EAS) AF: 0.697 AC: 3595 AN: 5158

South Asian (SAS) AF: 0.559 AC: 2676 AN: 4788

European-Finnish (FIN) AF: 0.611 AC: 6440 AN: 10532

Middle Eastern (MID) AF: 0.527 AC: 155 AN: 294

European-Non Finnish (NFE) AF: 0.580 AC: 39378 AN: 67938

Other (OTH) AF: 0.511 AC: 1074 AN: 2100

Alfa AF: 0.504 Hom.: 7322

Bravo AF: 0.469

Asia WGS AF: 0.609 AC: 2118 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.5
DANN	Benign	0.74
PhyloP100		0.35
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: rs17768343; hg19: chr14-38001181;