chr14-37248090-G-A

Variant names:

• chr14-37248090-G-A
• rs7150986
• NM_001388067.1:c.19+183G>A

Variant summary

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

The NM_001388067.1(MIPOL1):​c.19+183G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0391 in 151,370 control chromosomes in the GnomAD database, including 258 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 0.039 (258 hom., cov: 31)
• Consequence: MIPOL1 NM_001388067.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.326
• Publications: 1 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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.71).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.102 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MIPOL1	NM_001388067.1	c.19+183G>A		intron_variant	Intron 3 of 12	ENST00000684589.1	NP_001374996.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MIPOL1	ENST00000684589.1	c.19+183G>A		intron_variant	Intron 3 of 12		NM_001388067.1	ENSP00000506738.1

Frequencies

GnomAD3 genomes AF: 0.0390 AC: 5897 AN: 151252 Hom.: 256 Cov.: 31

Gnomad AFR AF: 0.104

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0166

Gnomad ASJ AF: 0.0297

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00500

Gnomad FIN AF: 0.0115

Gnomad MID AF: 0.0478

Gnomad NFE AF: 0.0153

Gnomad OTH AF: 0.0298

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

GnomAD4 genome AF: 0.0391 AC: 5922 AN: 151370 Hom.: 258 Cov.: 31 AF XY: 0.0384 AC XY: 2838 AN XY: 73978

African (AFR) AF: 0.105 AC: 4309 AN: 41218

American (AMR) AF: 0.0166 AC: 251 AN: 15164

Ashkenazi Jewish (ASJ) AF: 0.0297 AC: 103 AN: 3466

East Asian (EAS) AF: 0.00 AC: 0 AN: 5132

South Asian (SAS) AF: 0.00480 AC: 23 AN: 4792

European-Finnish (FIN) AF: 0.0115 AC: 121 AN: 10482

Middle Eastern (MID) AF: 0.0514 AC: 15 AN: 292

European-Non Finnish (NFE) AF: 0.0153 AC: 1038 AN: 67808

Other (OTH) AF: 0.0295 AC: 62 AN: 2104

Alfa AF: 0.0237 Hom.: 115

Bravo AF: 0.0428

Asia WGS AF: 0.00837 AC: 29 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	6.8
DANN	Benign	0.84
PhyloP100		-0.33
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: rs7150986; hg19: chr14-37717295;