6-53944181-C-G

Variant names:

• chr6-53944181-C-G
• rs7766181
• ENST00000431554.2:n.232+13904C>G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000505762.1(MLIP):​c.57+13904C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.521 in 151,922 control chromosomes in the GnomAD database, including 21,302 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 0.52 (21302 hom., cov: 32)
• Consequence: MLIP ENST00000505762.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.518

Genes affected

MLIP (HGNC:21355): (muscular LMNA interacting protein) Predicted to enable lamin binding activity and transcription corepressor activity. Predicted to be involved in negative regulation of cardiac muscle hypertrophy in response to stress; negative regulation of transcription by RNA polymerase II; and positive regulation of transcription by RNA polymerase II. Predicted to be located in nuclear lumen. Predicted to be active in PML body; nuclear envelope; and sarcolemma. [provided by Alliance of Genome Resources, Apr 2022]

LOC101927189 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.885 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101927189	NR_125842.1	n.296+13904C>G		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MLIP	ENST00000431554.2	n.232+13904C>G		intron_variant	Intron 1 of 3	1
MLIP	ENST00000505762.1	c.57+13904C>G		intron_variant	Intron 1 of 2	3		ENSP00000423191.1
MLIP	ENST00000511369.5	n.256+13904C>G		intron_variant	Intron 1 of 2	4

Frequencies

GnomAD3 genomes AF: 0.521 AC: 79032 AN: 151804 Hom.: 21275 Cov.: 32

Gnomad AFR AF: 0.517

Gnomad AMI AF: 0.613

Gnomad AMR AF: 0.613

Gnomad ASJ AF: 0.409

Gnomad EAS AF: 0.906

Gnomad SAS AF: 0.565

Gnomad FIN AF: 0.560

Gnomad MID AF: 0.437

Gnomad NFE AF: 0.469

Gnomad OTH AF: 0.498

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

GnomAD4 genome AF: 0.521 AC: 79106 AN: 151922 Hom.: 21302 Cov.: 32 AF XY: 0.528 AC XY: 39222 AN XY: 74262

Gnomad4 AFR AF: 0.517

Gnomad4 AMR AF: 0.614

Gnomad4 ASJ AF: 0.409

Gnomad4 EAS AF: 0.907

Gnomad4 SAS AF: 0.564

Gnomad4 FIN AF: 0.560

Gnomad4 NFE AF: 0.469

Gnomad4 OTH AF: 0.501

Alfa AF: 0.315 Hom.: 709

Bravo AF: 0.530

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	3.1
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7766181; hg19: chr6-53808979;