rs13382161

Positions:

• chr19-41136063-C-G

Variant summary

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

The XM_047439802.1(LOC124904790):​c.*673G>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.129 in 165,832 control chromosomes in the GnomAD database, including 2,102 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 0.13 (2025 hom., cov: 32)
  • Exomes 𝑓: 0.099 (77 hom.)
• Consequence: LOC124904790 XM_047439802.1 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.330

Genes affected

LOC124904790 (HGNC:):

CYP2T3P (HGNC:18853): (cytochrome P450 family 2 subfamily T member 3, pseudogene)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.268 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124904790	XM_047439802.1	c.*673G>C		3_prime_UTR_variant	3/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CYP2T3P	ENST00000601990.1	n.336C>G		non_coding_transcript_exon_variant	3/7

Frequencies

GnomAD3 genomes AF: 0.132 AC: 20017 AN: 152056 Hom.: 2016 Cov.: 32

Gnomad AFR AF: 0.272

Gnomad AMI AF: 0.0175

Gnomad AMR AF: 0.163

Gnomad ASJ AF: 0.0470

Gnomad EAS AF: 0.0226

Gnomad SAS AF: 0.0959

Gnomad FIN AF: 0.0716

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0670

Gnomad OTH AF: 0.0908

GnomAD4 exome AF: 0.0990 AC: 1352 AN: 13658 Hom.: 77 Cov.: 0 AF XY: 0.0963 AC XY: 710 AN XY: 7376

Gnomad4 AFR exome AF: 0.217

Gnomad4 AMR exome AF: 0.151

Gnomad4 ASJ exome AF: 0.0811

Gnomad4 EAS exome AF: 0.0190

Gnomad4 SAS exome AF: 0.122

Gnomad4 FIN exome AF: 0.0732

Gnomad4 NFE exome AF: 0.0908

Gnomad4 OTH exome AF: 0.0824

GnomAD4 genome AF: 0.132 AC: 20058 AN: 152174 Hom.: 2025 Cov.: 32 AF XY: 0.130 AC XY: 9703 AN XY: 74388

Gnomad4 AFR AF: 0.272

Gnomad4 AMR AF: 0.163

Gnomad4 ASJ AF: 0.0470

Gnomad4 EAS AF: 0.0226

Gnomad4 SAS AF: 0.0960

Gnomad4 FIN AF: 0.0716

Gnomad4 NFE AF: 0.0670

Gnomad4 OTH AF: 0.0899

Alfa AF: 0.0983 Hom.: 166

Bravo AF: 0.143

Asia WGS AF: 0.0640 AC: 225 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	8.1
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13382161; hg19: chr19-41641968;