ENST00000512519.2:n.165+364_165+365insT

Variant names:

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

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+365insT 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 0.41 (7335 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 (SAS) allele frequency at 95% confidence interval = 0.504 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
OSMR-DT	NR_109951.1	n.162+364dupT		intron_variant	Intron 1 of 3
OSMR-DT	NR_171676.1	n.102+364dupT		intron_variant	Intron 1 of 2
OSMR-DT	NR_171677.1	n.102+364dupT		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+365insT		intron_variant	Intron 1 of 1	2
OSMR-DT	ENST00000513480.2	n.107+364_107+365insT		intron_variant	Intron 1 of 3	4
OSMR-DT	ENST00000636516.3	n.151+364_151+365insT		intron_variant	Intron 1 of 5	5

Frequencies

GnomAD3 genomes AF: 0.405 AC: 36259 AN: 89500 Hom.: 7333 Cov.: 0

Gnomad AFR AF: 0.383

Gnomad AMI AF: 0.432

Gnomad AMR AF: 0.391

Gnomad ASJ AF: 0.459

Gnomad EAS AF: 0.277

Gnomad SAS AF: 0.527

Gnomad FIN AF: 0.320

Gnomad MID AF: 0.440

Gnomad NFE AF: 0.422

Gnomad OTH AF: 0.415

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

GnomAD4 genome AF: 0.405 AC: 36251 AN: 89482 Hom.: 7335 Cov.: 0 AF XY: 0.403 AC XY: 16578 AN XY: 41096

African (AFR) AF: 0.383 AC: 8400 AN: 21928

American (AMR) AF: 0.390 AC: 2931 AN: 7514

Ashkenazi Jewish (ASJ) AF: 0.459 AC: 1167 AN: 2544

East Asian (EAS) AF: 0.277 AC: 972 AN: 3506

South Asian (SAS) AF: 0.529 AC: 1275 AN: 2412

European-Finnish (FIN) AF: 0.320 AC: 866 AN: 2710

Middle Eastern (MID) AF: 0.436 AC: 68 AN: 156

European-Non Finnish (NFE) AF: 0.422 AC: 19795 AN: 46874

Other (OTH) AF: 0.418 AC: 486 AN: 1164

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;