rs587777363

Positions:

• chr5-162537506-A-ATGTTTACTAAACAAAAAGAAAGAGC

Variant summary

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

The XR_941159.2(LOC105377697):​n.1921+1323_1921+1324insGCTCTTTCTTTTTGTTTAGTAAACA variant causes a intron, non coding transcript 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 risk factor (no stars).

• Frequency: Genomes: not found (cov: 32)
• Consequence: LOC105377697 XR_941159.2 intron, non_coding_transcript
• Clinical Significance: risk factor no assertion criteria provided O:1
• Conservation: PhyloP100: -1.96

Genes affected

LOC105377697 (HGNC:):

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/exons	MANE	Protein	UniProt
LOC105377697	XR_941159.2	n.1921+1323_1921+1324insGCTCTTTCTTTTTGTTTAGTAAACA		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000644348.1	n.1689+1323_1689+1324insGCTCTTTCTTTTTGTTTAGTAAACA		intron_variant, non_coding_transcript_variant
	ENST00000646143.2	n.2620+9531_2620+9532insGCTCTTTCTTTTTGTTTAGTAAACA		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes Cov.: 32

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

GnomAD4 genome Cov.: 32

ClinVar

Significance: risk factor

Submissions summary: Other:1

Revision: no assertion criteria provided

Submissions by phenotype

Epilepsy, idiopathic generalized, susceptibility to, 13 Other:1

risk factor, no assertion criteria provided

literature only

OMIM

Jul 01, 2011

- -

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs587777363; hg19: chr5-161964512;