5-38845303-CAAAAAAAA-CAAAAAA

Variant names:

• chr5-38845303-CAA-C
• rs5867434
• ENST00000512519.2:n.165+363_165+364delTT

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The ENST00000512519.2(OSMR-DT):​n.165+363_165+364delTT 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 0.00012 (0 hom., cov: 0)
• Consequence: OSMR-DT ENST00000512519.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0280
• Publications: 1 publications found

Genes affected

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

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

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+363_162+364delTT		intron	N/A
	OSMR-DT	NR_171676.1		n.102+363_102+364delTT		intron	N/A
	OSMR-DT	NR_171677.1		n.102+363_102+364delTT		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OSMR-DT	ENST00000512519.2	TSL:2	n.165+363_165+364delTT		intron	N/A
	OSMR-DT	ENST00000513480.2	TSL:4	n.107+363_107+364delTT		intron	N/A
	OSMR-DT	ENST00000636516.3	TSL:5	n.151+363_151+364delTT		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.000123 AC: 11 AN: 89676 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.0000456

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000133

Gnomad ASJ AF: 0.000393

Gnomad EAS AF: 0.00141

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.000370

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000426

Gnomad OTH AF: 0.00

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

GnomAD4 genome AF: 0.000123 AC: 11 AN: 89656 Hom.: 0 Cov.: 0 AF XY: 0.000121 AC XY: 5 AN XY: 41156

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.0000455 AC: 1 AN: 21966

American (AMR) AF: 0.000133 AC: 1 AN: 7542

Ashkenazi Jewish (ASJ) AF: 0.000393 AC: 1 AN: 2542

East Asian (EAS) AF: 0.00142 AC: 5 AN: 3518

South Asian (SAS) AF: 0.00 AC: 0 AN: 2414

European-Finnish (FIN) AF: 0.000370 AC: 1 AN: 2702

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

European-Non Finnish (NFE) AF: 0.0000426 AC: 2 AN: 46970

Other (OTH) AF: 0.00 AC: 0 AN: 1168

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0.0000000876083), which strongly suggests a high chance of mosaicism in these individuals.

Alfa AF: 0.00 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		-0.028

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;