rs5867434

Positions:

• chr5-38845303-CAAAAAAAA-C
• chr5-38845303-CAAAAAAAA-CA
• chr5-38845303-CAAAAAAAA-CAAA
• chr5-38845303-CAAAAAAAA-CAAAA
• chr5-38845303-CAAAAAAAA-CAAAAAA
• chr5-38845303-CAAAAAAAA-CAAAAAAA
• chr5-38845303-CAAAAAAAA-CAAAAAAAAA
• chr5-38845303-CAAAAAAAA-CAAAAAAAAAA
• chr5-38845303-CAAAAAAAA-CAAAAAAAAAAA
• chr5-38845303-CAAAAAAAA-CAAAAAAAAAAAA
• chr5-38845303-CAAAAAAAA-CAAAAAAAAAAAAA
• chr5-38845303-CAAAAAAAA-CAAAAAAAAAAAAAA

Variant summary

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

The NR_109951.1(OSMR-DT):​n.162+357_162+364del variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.000011 (0 hom., cov: 0)
• Consequence: OSMR-DT NR_109951.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.228

Genes affected

OSMR-DT (HGNC:50296): (OSMR divergent transcript)

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
OSMR-DT	NR_109951.1	n.162+357_162+364del		intron_variant, non_coding_transcript_variant
OSMR-DT	NR_171676.1	n.102+357_102+364del		intron_variant, non_coding_transcript_variant
OSMR-DT	NR_171677.1	n.102+357_102+364del		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
OSMR-DT	ENST00000662290.1	n.126+357_126+364del		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0000111 AC: 1 AN: 89698 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.0000456

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

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

GnomAD4 genome AF: 0.0000112 AC: 1 AN: 89678 Hom.: 0 Cov.: 0 AF XY: 0.0000243 AC XY: 1 AN XY: 41172

Gnomad4 AFR AF: 0.0000455

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.00

Gnomad4 OTH AF: 0.00

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

LitVar

Other links and lift over

dbSNP: rs5867434; hg19: chr5-38845405;