5-38845303-CAAAAAAAA-CAAAAAAA

Variant names:

• chr5-38845303-CA-C
• rs5867434
• ENST00000512519.2:n.165+364delT

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The ENST00000512519.2(OSMR-DT):​n.165+364delT variant causes a intron 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 ENST00000512519.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.41
• Publications: 1 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000512519.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OSMR-DT	NR_109951.1		n.162+364delT		intron	N/A
	OSMR-DT	NR_171676.1		n.102+364delT		intron	N/A
	OSMR-DT	NR_171677.1		n.102+364delT		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OSMR-DT	ENST00000512519.2	TSL:2	n.165+364delT		intron	N/A
	OSMR-DT	ENST00000513480.2	TSL:4	n.107+364delT		intron	N/A
	OSMR-DT	ENST00000636516.3	TSL:5	n.151+364delT		intron	N/A

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

African (AFR) AF: 0.00665 AC: 146 AN: 21958

American (AMR) AF: 0.0203 AC: 153 AN: 7544

Ashkenazi Jewish (ASJ) AF: 0.0122 AC: 31 AN: 2542

East Asian (EAS) AF: 0.377 AC: 1318 AN: 3496

South Asian (SAS) AF: 0.0348 AC: 84 AN: 2412

European-Finnish (FIN) AF: 0.0107 AC: 29 AN: 2702

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 156

European-Non Finnish (NFE) AF: 0.0169 AC: 794 AN: 46966

Other (OTH) AF: 0.0472 AC: 55 AN: 1166

Alfa AF: 0.00 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		-1.4

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs5867434;

hg19: chr5-38845405;