1-147445799-T-C

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000606338.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00624	NR_038423.2		n.701-60936A>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00624	ENST00000619867.4	TSL:1	n.701-37110A>G		intron	N/A
	LINC00624	ENST00000621316.2	TSL:1	n.705-60936A>G		intron	N/A
	OR13Z2P	ENST00000606338.1	TSL:6	n.221T>C		non_coding_transcript_exon	Exon 1 of 1

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.500 AC: 1 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.647 AC: 22 AN: 34

Other (OTH) AF: 0.750 AC: 3 AN: 4

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

African (AFR) AF: 0.891 AC: 36994 AN: 41504

American (AMR) AF: 0.727 AC: 11111 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.497 AC: 1725 AN: 3472

East Asian (EAS) AF: 0.599 AC: 3073 AN: 5132

South Asian (SAS) AF: 0.617 AC: 2960 AN: 4800

European-Finnish (FIN) AF: 0.684 AC: 7225 AN: 10560

Middle Eastern (MID) AF: 0.619 AC: 182 AN: 294

European-Non Finnish (NFE) AF: 0.623 AC: 42349 AN: 67940

Other (OTH) AF: 0.668 AC: 1413 AN: 2114

Alfa AF: 0.631 Hom.: 3229

Bravo AF: 0.722

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	5.3
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs6688154; hg19: chr1-146917532;