1-147445799-T-C

Variant names:

• chr1-147445799-T-C
• rs6688154
• ENST00000619867.4:n.701-37110A>G

Variant summary

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

The ENST00000606338.1(OR13Z2P):​n.221T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.708 in 152,006 control chromosomes in the GnomAD database, including 39,245 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 0.71 (39245 hom., cov: 31)
  • Exomes 𝑓: 0.65 (8 hom.)
  • Failed GnomAD Quality Control
• Consequence: OR13Z2P ENST00000606338.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.213

Genes affected

LINC00624 (HGNC:44254): (long intergenic non-protein coding RNA 624)

OR13Z2P (HGNC:31241): (olfactory receptor family 13 subfamily Z member 2 pseudogene) 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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.884 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
OR13Z2P		n.147445799T>C		intragenic_variant
LINC00624	NR_038423.2	n.701-60936A>G		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00624	ENST00000619867.4	n.701-37110A>G		intron_variant	Intron 3 of 5	1
LINC00624	ENST00000621316.1	n.701-60936A>G		intron_variant	Intron 3 of 3	1
OR13Z2P	ENST00000606338.1	n.221T>C		non_coding_transcript_exon_variant	Exon 1 of 1	6

Frequencies

GnomAD3 genomes AF: 0.708 AC: 107547 AN: 151888 Hom.: 39175 Cov.: 31

Gnomad AFR AF: 0.891

Gnomad AMI AF: 0.709

Gnomad AMR AF: 0.727

Gnomad ASJ AF: 0.497

Gnomad EAS AF: 0.599

Gnomad SAS AF: 0.615

Gnomad FIN AF: 0.684

Gnomad MID AF: 0.614

Gnomad NFE AF: 0.623

Gnomad OTH AF: 0.670

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.650 AC: 26 AN: 40 Hom.: 8 Cov.: 0 AF XY: 0.636 AC XY: 14 AN XY: 22

Gnomad4 FIN exome AF: 0.500

Gnomad4 NFE exome AF: 0.647

Gnomad4 OTH exome AF: 0.750

GnomAD4 genome AF: 0.708 AC: 107679 AN: 152006 Hom.: 39245 Cov.: 31 AF XY: 0.709 AC XY: 52640 AN XY: 74290

Gnomad4 AFR AF: 0.891

Gnomad4 AMR AF: 0.727

Gnomad4 ASJ AF: 0.497

Gnomad4 EAS AF: 0.599

Gnomad4 SAS AF: 0.617

Gnomad4 FIN AF: 0.684

Gnomad4 NFE AF: 0.623

Gnomad4 OTH AF: 0.668

Alfa AF: 0.617 Hom.: 2929

Bravo AF: 0.722

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	5.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6688154; hg19: chr1-146917532;