chr1-147445799-T-C

Position:

• chr1-147445799-T-C

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:):

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/exons	MANE	Protein	UniProt
OR13Z2P		n.147445799T>C		intragenic_variant
LINC00624	NR_038423.2	n.701-60936A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC00624	ENST00000619867.4	n.701-37110A>G		intron_variant		1
LINC00624	ENST00000621316.1	n.701-60936A>G		intron_variant		1
OR13Z2P	ENST00000606338.1	n.221T>C		non_coding_transcript_exon_variant	1/1	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;