chr5-38845471-T-A

Variant names:

• chr5-38845471-T-A
• rs13359039
• ENST00000512519.2:n.165+197A>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000512519.2(OSMR-DT):​n.165+197A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0131 in 152,146 control chromosomes in the GnomAD database, including 52 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.013 (52 hom., cov: 33)
• Consequence: OSMR-DT ENST00000512519.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.690
• Publications: 1 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BS1: Variant frequency is greater than expected in population afr. GnomAd4 allele frequency = 0.0131 (1987/152146) while in subpopulation AFR AF = 0.0455 (1888/41488). AF 95% confidence interval is 0.0438. There are 52 homozygotes in GnomAd4. There are 940 alleles in the male GnomAd4 subpopulation. Median coverage is 33. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 52 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
OSMR-DT	NR_109951.1	n.162+197A>T		intron_variant	Intron 1 of 3
OSMR-DT	NR_171676.1	n.102+197A>T		intron_variant	Intron 1 of 2
OSMR-DT	NR_171677.1	n.102+197A>T		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+197A>T		intron_variant	Intron 1 of 1	2
OSMR-DT	ENST00000513480.2	n.107+197A>T		intron_variant	Intron 1 of 3	4
OSMR-DT	ENST00000636516.3	n.151+197A>T		intron_variant	Intron 1 of 5	5

Frequencies

GnomAD3 genomes AF: 0.0131 AC: 1987 AN: 152028 Hom.: 52 Cov.: 33

Gnomad AFR AF: 0.0456

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00439

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000208

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.0000882

Gnomad OTH AF: 0.0105

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

GnomAD4 genome AF: 0.0131 AC: 1987 AN: 152146 Hom.: 52 Cov.: 33 AF XY: 0.0126 AC XY: 940 AN XY: 74380

African (AFR) AF: 0.0455 AC: 1888 AN: 41488

American (AMR) AF: 0.00438 AC: 67 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3470

East Asian (EAS) AF: 0.00 AC: 0 AN: 5178

South Asian (SAS) AF: 0.000208 AC: 1 AN: 4814

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10598

Middle Eastern (MID) AF: 0.0102 AC: 3 AN: 294

European-Non Finnish (NFE) AF: 0.0000882 AC: 6 AN: 67994

Other (OTH) AF: 0.0104 AC: 22 AN: 2112

Alfa AF: 0.00 Hom.: 0

Bravo AF: 0.0153

Asia WGS AF: 0.00346 AC: 12 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.8
DANN	Benign	0.63
PhyloP100		-0.69
PromoterAI		-0.071	Neutral

Splicing

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

Other links and lift over

dbSNP: rs13359039; hg19: chr5-38845573;