19-9251064-CTTT-CTT

Variant names:

• chr19-9251064-CT-C
• rs201985790
• NM_001079935.2:c.32delT

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_001079935.2(OR7E24):​c.32delT​(p.Phe11SerfsTer89) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0149 in 1,074,790 control chromosomes in the GnomAD database, including 21 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.0011 (2 hom., cov: 32)
  • Exomes 𝑓: 0.017 (19 hom.)
• Consequence: OR7E24 NM_001079935.2 frameshift
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.465

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 Benign. Variant got -8 ACMG points.

• BA1: GnomAdExome4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0595 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
OR7E24	NM_001079935.2	c.32delT	p.Phe11SerfsTer89	frameshift_variant	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.32delT	p.Phe11SerfsTer89	frameshift_variant	Exon 1 of 1	6	NM_001079935.2	ENSP00000387523.1
OR7E24	ENST00000641946.1	c.30-10delT		intron_variant	Intron 1 of 1			ENSP00000494223.1

Frequencies

GnomAD3 genomes AF: 0.00106 AC: 157 AN: 147776 Hom.: 2 Cov.: 32

Gnomad AFR AF: 0.000867

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000271

Gnomad ASJ AF: 0.000293

Gnomad EAS AF: 0.0172

Gnomad SAS AF: 0.00149

Gnomad FIN AF: 0.000104

Gnomad MID AF: 0.00325

Gnomad NFE AF: 0.000270

Gnomad OTH AF: 0.000991

GnomAD4 exome AF: 0.0171 AC: 15823 AN: 926936 Hom.: 19 Cov.: 30 AF XY: 0.0182 AC XY: 8380 AN XY: 459658

Gnomad4 AFR exome AF: 0.0186

Gnomad4 AMR exome AF: 0.0394

Gnomad4 ASJ exome AF: 0.0236

Gnomad4 EAS exome AF: 0.0621

Gnomad4 SAS exome AF: 0.0259

Gnomad4 FIN exome AF: 0.0200

Gnomad4 NFE exome AF: 0.0137

Gnomad4 OTH exome AF: 0.0169

GnomAD4 genome AF: 0.00106 AC: 157 AN: 147854 Hom.: 2 Cov.: 32 AF XY: 0.000973 AC XY: 70 AN XY: 71948

Gnomad4 AFR AF: 0.000865

Gnomad4 AMR AF: 0.000270

Gnomad4 ASJ AF: 0.000293

Gnomad4 EAS AF: 0.0173

Gnomad4 SAS AF: 0.00150

Gnomad4 FIN AF: 0.000104

Gnomad4 NFE AF: 0.000270

Gnomad4 OTH AF: 0.000982

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;