5-38845303-CAAAAAAAA-CAAAAAAAAAA

Variant names:

• chr5-38845303-C-CAA
• rs5867434
• ENST00000512519.2:n.165+364_165+365insTT

Variant summary

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

The ENST00000512519.2(OSMR-DT):​n.165+364_165+365insTT 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 0.19 (1854 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 (NFE) allele frequency at 95% confidence interval = 0.198 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
OSMR-DT	NR_109951.1	n.162+363_162+364dupTT		intron_variant	Intron 1 of 3
OSMR-DT	NR_171676.1	n.102+363_102+364dupTT		intron_variant	Intron 1 of 2
OSMR-DT	NR_171677.1	n.102+363_102+364dupTT		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
OSMR-DT	ENST00000512519.2	n.165+364_165+365insTT		intron_variant	Intron 1 of 1	2
OSMR-DT	ENST00000513480.2	n.107+364_107+365insTT		intron_variant	Intron 1 of 3	4
OSMR-DT	ENST00000636516.3	n.151+364_151+365insTT		intron_variant	Intron 1 of 5	5

Frequencies

GnomAD3 genomes AF: 0.191 AC: 17076 AN: 89280 Hom.: 1853 Cov.: 0

Gnomad AFR AF: 0.191

Gnomad AMI AF: 0.189

Gnomad AMR AF: 0.189

Gnomad ASJ AF: 0.195

Gnomad EAS AF: 0.0728

Gnomad SAS AF: 0.180

Gnomad FIN AF: 0.189

Gnomad MID AF: 0.167

Gnomad NFE AF: 0.201

Gnomad OTH AF: 0.185

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

GnomAD4 genome AF: 0.191 AC: 17077 AN: 89262 Hom.: 1854 Cov.: 0 AF XY: 0.190 AC XY: 7771 AN XY: 40982

African (AFR) AF: 0.192 AC: 4189 AN: 21874

American (AMR) AF: 0.189 AC: 1426 AN: 7526

Ashkenazi Jewish (ASJ) AF: 0.195 AC: 493 AN: 2526

East Asian (EAS) AF: 0.0734 AC: 258 AN: 3516

South Asian (SAS) AF: 0.178 AC: 429 AN: 2404

European-Finnish (FIN) AF: 0.189 AC: 507 AN: 2688

Middle Eastern (MID) AF: 0.178 AC: 27 AN: 152

European-Non Finnish (NFE) AF: 0.201 AC: 9407 AN: 46738

Other (OTH) AF: 0.183 AC: 213 AN: 1162

Alfa AF: 0.00 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs5867434; hg19: chr5-38845405;