rs1409104

Variant names:

• chr6-54004652-C-T
• rs1409104
• ENST00000505762.1:c.150+21802C>T

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000505762.1(MLIP):​c.150+21802C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.429 in 151,976 control chromosomes in the GnomAD database, including 14,720 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 0.43 (14720 hom., cov: 32)
• Consequence: MLIP ENST00000505762.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.615
• Publications: 4 publications found

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]

MLIP-AS1 (HGNC:40963): (MLIP antisense RNA 1)

MLIP-IT1 (HGNC:41461): (MLIP intronic transcript 1)

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.23).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.487 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000505762.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MLIP-IT1	NR_046832.1		n.461+1933C>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MLIP	ENST00000505762.1	TSL:3	c.150+21802C>T		intron	N/A	ENSP00000423191.1
	MLIP	ENST00000441845.2	TSL:2	n.525+1933C>T		intron	N/A
	MLIP-AS1	ENST00000626297.2	TSL:5	n.193-15500G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.429 AC: 65170 AN: 151858 Hom.: 14725 Cov.: 32

Gnomad AFR AF: 0.355

Gnomad AMI AF: 0.657

Gnomad AMR AF: 0.368

Gnomad ASJ AF: 0.467

Gnomad EAS AF: 0.0869

Gnomad SAS AF: 0.442

Gnomad FIN AF: 0.536

Gnomad MID AF: 0.442

Gnomad NFE AF: 0.491

Gnomad OTH AF: 0.441

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

GnomAD4 genome AF: 0.429 AC: 65170 AN: 151976 Hom.: 14720 Cov.: 32 AF XY: 0.427 AC XY: 31678 AN XY: 74260

African (AFR) AF: 0.354 AC: 14690 AN: 41444

American (AMR) AF: 0.367 AC: 5594 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.467 AC: 1619 AN: 3468

East Asian (EAS) AF: 0.0867 AC: 449 AN: 5180

South Asian (SAS) AF: 0.441 AC: 2122 AN: 4816

European-Finnish (FIN) AF: 0.536 AC: 5660 AN: 10556

Middle Eastern (MID) AF: 0.434 AC: 126 AN: 290

European-Non Finnish (NFE) AF: 0.491 AC: 33395 AN: 67948

Other (OTH) AF: 0.435 AC: 918 AN: 2108

Alfa AF: 0.457 Hom.: 2042

Bravo AF: 0.414

Asia WGS AF: 0.269 AC: 934 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.23
CADD	Benign	17
DANN	Benign	0.73
PhyloP100		0.61

Splicing

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

Other links and lift over

dbSNP: rs1409104; hg19: chr6-53869450;