3-100451757-T-TGGAATTCCGATGCCGATCGTCTGACCGTCTTCCTAGAAGGCATTCTCATGAGGACCA

Position:

• chr3-100451757-T-TGGAATTCCGATGCCGATCGTCTGACCGTCTTCCTAGAAGGCATTCTCATGAGGACCA

Variant summary

Our verdict is Uncertain significance. Variant got 3 ACMG points: 4P and 1B. PM2 PM4 BP6

The NM_001085451.2(LNP1):​c.195_196insGGAATTCCGATGCCGATCGTCTGACCGTCTTCCTAGAAGGCATTCTCATGAGGACCA​(p.His65_Pro66insGlyIleProMetProIleValTerProSerSerTerLysAlaPheSerTerGlyPro) variant causes a stop gained, conservative inframe insertion change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Benign (no stars). Variant results in nonsense mediated mRNA decay.

• Frequency: Genomes: not found (cov: 39)
• Consequence: LNP1 NM_001085451.2 stop_gained, conservative_inframe_insertion
• Clinical Significance: Benign no assertion criteria provided B:1
• Conservation: PhyloP100: 0.250

Genes affected

LNP1 (HGNC:28014): (leukemia NUP98 fusion partner 1)

ACMG classification

Verdict is Uncertain_significance. Variant got 3 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PM4: Nonframeshift variant in NON repetitive region in NM_001085451.2.
• BP6: Variant 3-100451757-T-TGGAATTCCGATGCCGATCGTCTGACCGTCTTCCTAGAAGGCATTCTCATGAGGACCA is Benign according to our data. Variant chr3-100451757-T-TGGAATTCCGATGCCGATCGTCTGACCGTCTTCCTAGAAGGCATTCTCATGAGGACCA is described in ClinVar as [Benign]. Clinvar id is 1687739.Status of the report is no_assertion_criteria_provided, 0 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LNP1	NM_001085451.2	c.195_196insGGAATTCCGATGCCGATCGTCTGACCGTCTTCCTAGAAGGCATTCTCATGAGGACCA	p.His65_Pro66insGlyIleProMetProIleValTerProSerSerTerLysAlaPheSerTerGlyPro	stop_gained, conservative_inframe_insertion	3/4	ENST00000383693.8	NP_001078920.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LNP1	ENST00000383693.8	c.195_196insGGAATTCCGATGCCGATCGTCTGACCGTCTTCCTAGAAGGCATTCTCATGAGGACCA	p.His65_Pro66insGlyIleProMetProIleValTerProSerSerTerLysAlaPheSerTerGlyPro	stop_gained, conservative_inframe_insertion	3/4	1	NM_001085451.2	ENSP00000373191.3
LNP1	ENST00000489752.1	c.234_235insGGAATTCCGATGCCGATCGTCTGACCGTCTTCCTAGAAGGCATTCTCATGAGGACCA	p.His78_Pro79insGlyIleProMetProIleValTerProSerSerTerLysAlaPheSerTerGlyPro	stop_gained, conservative_inframe_insertion	3/4	5		ENSP00000417985.1
LNP1	ENST00000466996.5	n.*7_*8insGGAATTCCGATGCCGATCGTCTGACCGTCTTCCTAGAAGGCATTCTCATGAGGACCA		non_coding_transcript_exon_variant	3/4	5		ENSP00000419213.1
LNP1	ENST00000466996.5	n.*7_*8insGGAATTCCGATGCCGATCGTCTGACCGTCTTCCTAGAAGGCATTCTCATGAGGACCA		3_prime_UTR_variant	3/4	5		ENSP00000419213.1

Frequencies

GnomAD3 genomes Cov.: 39

GnomAD4 exome Cov.: 39

GnomAD4 genome Cov.: 39

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

Submissions by phenotype

Neurodevelopmental disorder with epilepsy and hypoplasia of the corpus callosum Benign:1

Benign, no assertion criteria provided

clinical testing

Molecular Genetics, Sadra Medical Genetics Laboratory

May 30, 2022

please look at the following link (normal Iranian population genetic databases: http://www.iranome.ir) rs71132521 http://www.iranome.ir/variant/3-100170601-_-TCCTAGAAGGCATTCTCATGAGGACCAGGAATTCCGATGCCGATCGTCTGACCGTCT MAF:0.4606 -

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr3-100170601;