11-5552350-T-G

Position:

• chr11-5552350-T-G

Variant summary

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

The ENST00000380259.7(ENSG00000239920):​n.*739+38475A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.236 in 153,936 control chromosomes in the GnomAD database, including 4,523 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 0.24 (4472 hom., cov: 32)
  • Exomes 𝑓: 0.22 (51 hom.)
• Consequence: ENSG00000239920 ENST00000380259.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.12

Genes affected

ENSG00000239920 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.272 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
OR52H2P		n.5552350T>G		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000239920	ENST00000380259.7	n.*739+38475A>C		intron_variant		5		ENSP00000369609.3
OR52H2P	ENST00000514607.1	n.214A>C		non_coding_transcript_exon_variant	1/1	6

Frequencies

GnomAD3 genomes AF: 0.237 AC: 35939 AN: 151870 Hom.: 4467 Cov.: 32

Gnomad AFR AF: 0.193

Gnomad AMI AF: 0.244

Gnomad AMR AF: 0.275

Gnomad ASJ AF: 0.333

Gnomad EAS AF: 0.0794

Gnomad SAS AF: 0.117

Gnomad FIN AF: 0.205

Gnomad MID AF: 0.282

Gnomad NFE AF: 0.275

Gnomad OTH AF: 0.242

GnomAD4 exome AF: 0.225 AC: 438 AN: 1948 Hom.: 51 Cov.: 0 AF XY: 0.253 AC XY: 276 AN XY: 1090

Gnomad4 AFR exome AF: 0.231

Gnomad4 AMR exome AF: 0.500

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.500

Gnomad4 SAS exome AF: 0.111

Gnomad4 FIN exome AF: 0.212

Gnomad4 NFE exome AF: 0.219

Gnomad4 OTH exome AF: 0.303

GnomAD4 genome AF: 0.237 AC: 35962 AN: 151988 Hom.: 4472 Cov.: 32 AF XY: 0.232 AC XY: 17235 AN XY: 74298

Gnomad4 AFR AF: 0.193

Gnomad4 AMR AF: 0.275

Gnomad4 ASJ AF: 0.333

Gnomad4 EAS AF: 0.0795

Gnomad4 SAS AF: 0.116

Gnomad4 FIN AF: 0.205

Gnomad4 NFE AF: 0.275

Gnomad4 OTH AF: 0.244

Alfa AF: 0.233 Hom.: 2204

Bravo AF: 0.237

Asia WGS AF: 0.117 AC: 406 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	5.6
DANN	Benign	0.65

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs10500651; hg19: chr11-5573580;