rs13382161

Variant names:

• chr19-41136063-C-G
• rs13382161
• ENST00000601990.1:n.336C>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000601990.1(CYP2T3P):​n.336C>G 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 0.129 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: CYP2T3P ENST00000601990.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.330
• Publications: 1 publications found

Genes affected

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

ENSG00000301076 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
CYP2T3P		n.41136063C>G		intragenic_variant
LOC124904790	XM_047439802.1	c.*673G>C		3_prime_UTR_variant	Exon 3 of 3		XP_047295758.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CYP2T3P	ENST00000601990.1	n.336C>G		non_coding_transcript_exon_variant	Exon 3 of 7	6
ENSG00000301076	ENST00000775977.1	n.51C>G		non_coding_transcript_exon_variant	Exon 1 of 3
ENSG00000301056	ENST00000775808.1	n.557+310G>C		intron_variant	Intron 3 of 3

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

African (AFR) AF: 0.217 AC: 69 AN: 318

American (AMR) AF: 0.151 AC: 175 AN: 1158

Ashkenazi Jewish (ASJ) AF: 0.0811 AC: 18 AN: 222

East Asian (EAS) AF: 0.0190 AC: 7 AN: 368

South Asian (SAS) AF: 0.122 AC: 197 AN: 1620

European-Finnish (FIN) AF: 0.0732 AC: 52 AN: 710

Middle Eastern (MID) AF: 0.0556 AC: 2 AN: 36

European-Non Finnish (NFE) AF: 0.0908 AC: 774 AN: 8522

Other (OTH) AF: 0.0824 AC: 58 AN: 704

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

African (AFR) AF: 0.272 AC: 11286 AN: 41508

American (AMR) AF: 0.163 AC: 2493 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0470 AC: 163 AN: 3466

East Asian (EAS) AF: 0.0226 AC: 117 AN: 5174

South Asian (SAS) AF: 0.0960 AC: 463 AN: 4824

European-Finnish (FIN) AF: 0.0716 AC: 759 AN: 10604

Middle Eastern (MID) AF: 0.0442 AC: 13 AN: 294

European-Non Finnish (NFE) AF: 0.0670 AC: 4558 AN: 67980

Other (OTH) AF: 0.0899 AC: 190 AN: 2114

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
PhyloP100		-0.33

Splicing

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

Other links and lift over

dbSNP: rs13382161; hg19: chr19-41641968;