chr11-4475616-C-T

Position:

• chr11-4475616-C-T

Variant summary

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

The ENST00000641797.4(ENSG00000291144):​n.1415C>T 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 0.291 in 608,732 control chromosomes in the GnomAD database, including 26,586 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 0.27 (5949 hom., cov: 32)
  • Exomes 𝑓: 0.30 (20637 hom.)
• Consequence: ENSG00000291144 ENST00000641797.4 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.88

Genes affected

OR52K3P (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.351 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
OR52K3P		n.4475616C>T		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
OR52K3P	ENST00000531655.1	n.804C>T		non_coding_transcript_exon_variant	1/1	6
ENSG00000291144	ENST00000641797.4	n.1415C>T		non_coding_transcript_exon_variant	3/3
ENSG00000291144	ENST00000690343.1	n.1220C>T		non_coding_transcript_exon_variant	2/2

Frequencies

GnomAD3 genomes AF: 0.272 AC: 41358 AN: 151914 Hom.: 5938 Cov.: 32

Gnomad AFR AF: 0.185

Gnomad AMI AF: 0.324

Gnomad AMR AF: 0.281

Gnomad ASJ AF: 0.229

Gnomad EAS AF: 0.365

Gnomad SAS AF: 0.249

Gnomad FIN AF: 0.389

Gnomad MID AF: 0.210

Gnomad NFE AF: 0.302

Gnomad OTH AF: 0.279

GnomAD4 exome AF: 0.297 AC: 135712 AN: 456698 Hom.: 20637 Cov.: 4 AF XY: 0.294 AC XY: 71838 AN XY: 244172

Gnomad4 AFR exome AF: 0.180

Gnomad4 AMR exome AF: 0.322

Gnomad4 ASJ exome AF: 0.217

Gnomad4 EAS exome AF: 0.339

Gnomad4 SAS exome AF: 0.260

Gnomad4 FIN exome AF: 0.378

Gnomad4 NFE exome AF: 0.298

Gnomad4 OTH exome AF: 0.286

GnomAD4 genome AF: 0.272 AC: 41397 AN: 152034 Hom.: 5949 Cov.: 32 AF XY: 0.275 AC XY: 20390 AN XY: 74280

Gnomad4 AFR AF: 0.185

Gnomad4 AMR AF: 0.283

Gnomad4 ASJ AF: 0.229

Gnomad4 EAS AF: 0.365

Gnomad4 SAS AF: 0.249

Gnomad4 FIN AF: 0.389

Gnomad4 NFE AF: 0.302

Gnomad4 OTH AF: 0.278

Alfa AF: 0.294 Hom.: 14454

Bravo AF: 0.265

Asia WGS AF: 0.313 AC: 1088 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	16
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2278170; hg19: chr11-4496846;