chr10-45258725-C-T

Position:

• chr10-45258725-C-T

Variant summary

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

The ENST00000641007.1(OR6D1P):​n.763C>T variant causes a non coding transcript exon change. The variant allele was found at a frequency of 0.459 in 152,186 control chromosomes in the GnomAD database, including 17,561 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 0.46 (17531 hom., cov: 32)
  • Exomes 𝑓: 0.62 (30 hom.)
• Consequence: OR6D1P ENST00000641007.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 5.56

Genes affected

OR6D1P (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.5).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.548 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
OR6D1P		n.45258725C>T		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
OR6D1P	ENST00000436165.1	n.541C>T		non_coding_transcript_exon_variant	1/1	6
OR6D1P	ENST00000641007.1	n.763C>T		non_coding_transcript_exon_variant	2/2
OR6D1P	ENST00000641209.1	n.333C>T		non_coding_transcript_exon_variant	2/2

Frequencies

GnomAD3 genomes AF: 0.459 AC: 69787 AN: 151920 Hom.: 17526 Cov.: 32

Gnomad AFR AF: 0.260

Gnomad AMI AF: 0.682

Gnomad AMR AF: 0.455

Gnomad ASJ AF: 0.476

Gnomad EAS AF: 0.385

Gnomad SAS AF: 0.402

Gnomad FIN AF: 0.678

Gnomad MID AF: 0.551

Gnomad NFE AF: 0.552

Gnomad OTH AF: 0.476

GnomAD4 exome AF: 0.623 AC: 91 AN: 146 Hom.: 30 Cov.: 0 AF XY: 0.568 AC XY: 50 AN XY: 88

Gnomad4 AFR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.250

Gnomad4 EAS exome AF: 0.500

Gnomad4 FIN exome AF: 0.694

Gnomad4 NFE exome AF: 0.628

Gnomad4 OTH exome AF: 0.900

GnomAD4 genome AF: 0.459 AC: 69825 AN: 152040 Hom.: 17531 Cov.: 32 AF XY: 0.465 AC XY: 34596 AN XY: 74322

Gnomad4 AFR AF: 0.260

Gnomad4 AMR AF: 0.455

Gnomad4 ASJ AF: 0.476

Gnomad4 EAS AF: 0.386

Gnomad4 SAS AF: 0.402

Gnomad4 FIN AF: 0.678

Gnomad4 NFE AF: 0.552

Gnomad4 OTH AF: 0.477

Alfa AF: 0.463 Hom.: 2950

Bravo AF: 0.432

Asia WGS AF: 0.413 AC: 1437 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.50
CADD	Benign	14
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1890739; hg19: chr10-45754173;