5-38845303-CAAAAAAAA-CAAAAAAA

Position:

• chr5-38845303-CAAAAAAAA-CAAAAAAA

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NR_109951.1(OSMR-DT):​n.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 0.029 (180 hom., cov: 0)
• Consequence: OSMR-DT NR_109951.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.41

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.36 is higher than 0.05.

Transcripts

RefSeq

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

Frequencies

GnomAD3 genomes AF: 0.0293 AC: 2627 AN: 89640 Hom.: 181 Cov.: 0

Gnomad AFR AF: 0.00666

Gnomad AMI AF: 0.00885

Gnomad AMR AF: 0.0203

Gnomad ASJ AF: 0.0122

Gnomad EAS AF: 0.378

Gnomad SAS AF: 0.0357

Gnomad FIN AF: 0.0107

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0169

Gnomad OTH AF: 0.0458

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

GnomAD4 genome AF: 0.0292 AC: 2616 AN: 89620 Hom.: 180 Cov.: 0 AF XY: 0.0313 AC XY: 1287 AN XY: 41142

Gnomad4 AFR AF: 0.00665

Gnomad4 AMR AF: 0.0203

Gnomad4 ASJ AF: 0.0122

Gnomad4 EAS AF: 0.377

Gnomad4 SAS AF: 0.0348

Gnomad4 FIN AF: 0.0107

Gnomad4 NFE AF: 0.0169

Gnomad4 OTH AF: 0.0472

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;