9-92419157-A-T

Variant names:

• chr9-92419157-A-T
• rs2761678
• NM_005014.3:c.-16-1583T>A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_005014.3(OMD):​c.-16-1583T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.104 in 152,070 control chromosomes in the GnomAD database, including 875 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 0.10 (875 hom., cov: 31)
• Consequence: OMD NM_005014.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.672

Genes affected

OMD (HGNC:8134): (osteomodulin) Predicted to be involved in cell adhesion and regulation of bone mineralization. Located in extracellular exosome. [provided by Alliance of Genome Resources, Apr 2022]

CENPP (HGNC:32933): (centromere protein P) CENPP is a subunit of a CENPH (MIM 605607)-CENPI (MIM 300065)-associated centromeric complex that targets CENPA (MIM 117139) to centromeres and is required for proper kinetochore function and mitotic progression (Okada et al., 2006 [PubMed 16622420]).[supplied by OMIM, Mar 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.11 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
OMD	NM_005014.3	c.-16-1583T>A		intron_variant	Intron 1 of 2	ENST00000375550.5	NP_005005.1
CENPP	NM_001012267.3	c.564+39298A>T		intron_variant	Intron 5 of 7	ENST00000375587.8	NP_001012267.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
OMD	ENST00000375550.5	c.-16-1583T>A		intron_variant	Intron 1 of 2	1	NM_005014.3	ENSP00000364700.4
CENPP	ENST00000375587.8	c.564+39298A>T		intron_variant	Intron 5 of 7	1	NM_001012267.3	ENSP00000364737.3

Frequencies

GnomAD3 genomes AF: 0.104 AC: 15740 AN: 151952 Hom.: 874 Cov.: 31

Gnomad AFR AF: 0.0888

Gnomad AMI AF: 0.0932

Gnomad AMR AF: 0.104

Gnomad ASJ AF: 0.134

Gnomad EAS AF: 0.0918

Gnomad SAS AF: 0.0730

Gnomad FIN AF: 0.114

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.112

Gnomad OTH AF: 0.112

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

GnomAD4 genome AF: 0.104 AC: 15742 AN: 152070 Hom.: 875 Cov.: 31 AF XY: 0.103 AC XY: 7652 AN XY: 74332

Gnomad4 AFR AF: 0.0887

Gnomad4 AMR AF: 0.104

Gnomad4 ASJ AF: 0.134

Gnomad4 EAS AF: 0.0922

Gnomad4 SAS AF: 0.0714

Gnomad4 FIN AF: 0.114

Gnomad4 NFE AF: 0.112

Gnomad4 OTH AF: 0.109

Alfa AF: 0.0474 Hom.: 42

Bravo AF: 0.102

Asia WGS AF: 0.0640 AC: 221 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.068
DANN	Benign	0.32

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs2761678; hg19: chr9-95181439;