3-194646248-GGA-GGAGA

Variant names:

• chr3-194646248-G-GGA
• NM_018385.3:c.1544-7_1544-6dupTC

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_018385.3(LSG1):​c.1544-7_1544-6dupTC variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 32)
• Consequence: LSG1 NM_018385.3 splice_region, intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.855

Genes affected

LSG1 (HGNC:25652): (large 60S subunit nuclear export GTPase 1) This gene encodes a protein related to the yeast large subunit GTPase 1. The encoded protein is necessary for cell viability and may localize in the endoplasmic reticulum, nucleus and cytoplasm.[provided by RefSeq, Feb 2009]

TMEM44-AS2 (HGNC:41082): (TMEM44 antisense RNA 2)

ACMG classification

Verdict is Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LSG1	NM_018385.3	c.1544-7_1544-6dupTC		splice_region_variant, intron_variant	Intron 11 of 13	ENST00000265245.10	NP_060855.2
TMEM44-AS2	NR_186047.1	n.1819_1820dupGA		non_coding_transcript_exon_variant	Exon 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LSG1	ENST00000265245.10	c.1544-7_1544-6dupTC		splice_region_variant, intron_variant	Intron 11 of 13	1	NM_018385.3	ENSP00000265245.5
LSG1	ENST00000437613.1	c.692-7_692-6dupTC		splice_region_variant, intron_variant	Intron 4 of 5	5		ENSP00000408264.1
LSG1	ENST00000475763.5	n.195_196dupTC		non_coding_transcript_exon_variant	Exon 1 of 3	3
LSG1	ENST00000460584.1	n.340-7_340-6dupTC		splice_region_variant, intron_variant	Intron 1 of 3	2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 30

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

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: chr3-194366977;