rs201985790

Variant names:

• chr19-9251064-CTTT-C
• rs201985790
• NM_001079935.2:c.30_32delTTT

Your query was ambiguous. Multiple possible variants found:

• chr19-9251064-CTTT-C
• chr19-9251064-CTTT-CT
• chr19-9251064-CTTT-CTT
• chr19-9251064-CTTT-CTTTT
• chr19-9251064-CTTT-CTTTTT

Variant summary

Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2 PM4_Supporting

The NM_001079935.2(OR7E24):​c.30_32delTTT​(p.Phe11del) variant causes a disruptive inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000104 in 1,054,028 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 0.000010 (0 hom.)
• Consequence: OR7E24 NM_001079935.2 disruptive_inframe_deletion
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0900

Genes affected

OR7E24 (HGNC:8396): (olfactory receptor family 7 subfamily E member 24) 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 Uncertain_significance. Variant got 3 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PM4: Nonframeshift variant in NON repetitive region in NM_001079935.2. Strenght limited to Supporting due to length of the change: 1aa.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
OR7E24	NM_001079935.2	c.30_32delTTT	p.Phe11del	disruptive_inframe_deletion	Exon 1 of 1	ENST00000456448.3	NP_001073404.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
OR7E24	ENST00000456448.3	c.30_32delTTT	p.Phe11del	disruptive_inframe_deletion	Exon 1 of 1	6	NM_001079935.2	ENSP00000387523.1
OR7E24	ENST00000641946.1	c.30-12_30-10delTTT		intron_variant	Intron 1 of 1			ENSP00000494223.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 0.0000104 AC: 11 AN: 1054028 Hom.: 0 AF XY: 0.00000763 AC XY: 4 AN XY: 523934

Gnomad4 AFR exome AF: 0.0000415

Gnomad4 AMR exome AF: 0.0000974

Gnomad4 ASJ exome AF: 0.0000546

Gnomad4 EAS exome AF: 0.0000343

Gnomad4 SAS exome AF: 0.0000161

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00000374

Gnomad4 OTH exome AF: 0.0000230

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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: rs201985790; hg19: chr19-9361740;