rs7143938

Variant names:

• chr14-37246853-A-G
• rs7143938
• NM_001388067.1:c.-198-250A>G

Your query was ambiguous. Multiple possible variants found:

• chr14-37246853-A-G
• chr14-37246853-A-T

Variant summary

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

The NM_001388067.1(MIPOL1):​c.-198-250A>G variant causes a intron change. The variant allele was found at a frequency of 0.298 in 151,908 control chromosomes in the GnomAD database, including 6,961 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 0.30 (6961 hom., cov: 32)
• Consequence: MIPOL1 NM_001388067.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.12
• Publications: 5 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=-0.49).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.428 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MIPOL1	NM_001388067.1	c.-198-250A>G		intron_variant	Intron 1 of 12	ENST00000684589.1	NP_001374996.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MIPOL1	ENST00000684589.1	c.-198-250A>G		intron_variant	Intron 1 of 12		NM_001388067.1	ENSP00000506738.1

Frequencies

GnomAD3 genomes AF: 0.298 AC: 45240 AN: 151790 Hom.: 6947 Cov.: 32

Gnomad AFR AF: 0.238

Gnomad AMI AF: 0.224

Gnomad AMR AF: 0.369

Gnomad ASJ AF: 0.300

Gnomad EAS AF: 0.442

Gnomad SAS AF: 0.363

Gnomad FIN AF: 0.263

Gnomad MID AF: 0.283

Gnomad NFE AF: 0.309

Gnomad OTH AF: 0.311

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

GnomAD4 genome AF: 0.298 AC: 45264 AN: 151908 Hom.: 6961 Cov.: 32 AF XY: 0.300 AC XY: 22253 AN XY: 74242

African (AFR) AF: 0.237 AC: 9846 AN: 41476

American (AMR) AF: 0.369 AC: 5632 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.300 AC: 1041 AN: 3470

East Asian (EAS) AF: 0.443 AC: 2290 AN: 5168

South Asian (SAS) AF: 0.363 AC: 1750 AN: 4818

European-Finnish (FIN) AF: 0.263 AC: 2787 AN: 10582

Middle Eastern (MID) AF: 0.284 AC: 83 AN: 292

European-Non Finnish (NFE) AF: 0.309 AC: 20980 AN: 67836

Other (OTH) AF: 0.309 AC: 651 AN: 2110

Alfa AF: 0.292 Hom.: 1131

Bravo AF: 0.304

Asia WGS AF: 0.389 AC: 1350 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.49
CADD	Benign	20
DANN	Benign	0.89
PhyloP100		4.1
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: rs7143938; hg19: chr14-37716058;