11-56699609-T-C

Position:

• chr11-56699609-T-C

Variant summary

Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4_Strong BP6

The NM_001005213.2(OR9G1):​c.-19+419T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars).

• Frequency:
  • Genomes: 𝑓 0.50 (250 hom., cov: 42)
  • Failed GnomAD Quality Control
• Consequence: OR9G1 NM_001005213.2 intron
• Clinical Significance: Likely benign no assertion criteria provided B:1
• Conservation: PhyloP100: -0.845

Genes affected

OR9G1 (HGNC:15319): (olfactory receptor family 9 subfamily G member 1) Olfactory receptors interact with odorant molecules in the nose, to initiate a neuronal response that triggers the perception of a smell. The olfactory receptor proteins are members of a large family of G-protein-coupled receptors (GPCR) arising from single coding-exon genes. Olfactory receptors share a 7-transmembrane domain structure with many neurotransmitter and hormone receptors and are responsible for the recognition and G protein-mediated transduction of odorant signals. The olfactory receptor gene family is the largest in the genome. The nomenclature assigned to the olfactory receptor genes and proteins for this organism is independent of other organisms. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Likely_benign. Variant got -5 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BP6: Variant 11-56699609-T-C is Benign according to our data. Variant chr11-56699609-T-C is described in ClinVar as [Likely_benign]. Clinvar id is 873252.Status of the report is no_assertion_criteria_provided, 0 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
OR9G1	NM_001005213.2	c.-19+419T>C		intron_variant		ENST00000642097.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
OR9G1	ENST00000642097.1	c.-19+419T>C		intron_variant			NM_001005213.2	P1

Frequencies

GnomAD3 genomes AF: 0.00 AC: 50632 AN: 101128 Hom.: 249 Cov.: 42 FAILED QC

Gnomad AFR AF: 0.502

Gnomad AMI AF: 0.500

Gnomad AMR AF: 0.497

Gnomad ASJ AF: 0.500

Gnomad EAS AF: 0.496

Gnomad SAS AF: 0.498

Gnomad FIN AF: 0.501

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.500

Gnomad OTH AF: 0.501

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

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.501 AC: 50673 AN: 101212 Hom.: 250 Cov.: 42 AF XY: 0.501 AC XY: 24572 AN XY: 49092

Gnomad4 AFR AF: 0.502

Gnomad4 AMR AF: 0.497

Gnomad4 ASJ AF: 0.500

Gnomad4 EAS AF: 0.496

Gnomad4 SAS AF: 0.498

Gnomad4 FIN AF: 0.501

Gnomad4 NFE AF: 0.500

Gnomad4 OTH AF: 0.499

Alfa AF: 0.429 Hom.: 8308

Asia WGS AF: 0.289 AC: 1000 AN: 3466

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

Submissions by phenotype

not specified Benign:1

Likely benign, no assertion criteria provided

case-control

Suna and Inan Kirac Foundation Neurodegeneration Research Laboratory, Koc University

Apr 02, 2020

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.4
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10896513; hg19: chr11-56467085;