rs13382161

Variant names:

• chr19-41136063-C-G
• rs13382161
• XM_047439802.1:c.*673G>C

Variant summary

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

The ENST00000775977.1(ENSG00000301076):​n.51C>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: ENSG00000301076 ENST00000775977.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.330
• Publications: 1 publications found

Genes affected

LOC124904790 (HGNC:):

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

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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000775977.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CYP2T3P	ENST00000601990.1	TSL:6	n.336C>G		non_coding_transcript_exon	Exon 3 of 7
	ENSG00000301076	ENST00000775977.1		n.51C>G		non_coding_transcript_exon	Exon 1 of 3
	ENSG00000301056	ENST00000775808.1		n.557+310G>C		intron	N/A

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs13382161;

hg19: chr19-41641968;