rs17768343

chr14-37531976-A-Cchr14-37531976-A-T

Variant summary

Our verdict is Benign. Variant got -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

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]

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
MIPOL1	NM_001388067.1	c.1263-14929A>C		intron_variant		ENST00000684589.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MIPOL1	ENST00000684589.1	c.1263-14929A>C		intron_variant			NM_001388067.1	P1

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

Gnomad4 AFR AF: 0.217

Gnomad4 AMR AF: 0.537

Gnomad4 ASJ AF: 0.559

Gnomad4 EAS AF: 0.697

Gnomad4 SAS AF: 0.559

Gnomad4 FIN AF: 0.611

Gnomad4 NFE AF: 0.580

Gnomad4 OTH AF: 0.511

Alfa AF: 0.501 Hom.: 6409

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

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: rs17768343; hg19: chr14-38001181;