rs10405596

chr19-40808815-C-T

Variant summary

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

The NR_144551.1(CYP2T1P):n.2197G>A 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 0.185 in 152,644 control chromosomes in the GnomAD database, including 2,912 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 0.18 (2907 hom., cov: 33)
  • Exomes 𝑓: 0.15 (5 hom.)
• Consequence: CYP2T1P NR_144551.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.305

Genes affected

CYP2T1P (HGNC:18852): (cytochrome P450 family 2 subfamily T member 1, pseudogene)

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 (AFR) allele frequency at 95% confidence interval = 0.277 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CYP2T1P	NR_144551.1	n.2197G>A		non_coding_transcript_exon_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CYP2T1P	ENST00000432607.2	n.1246G>A		non_coding_transcript_exon_variant	8/9
CYP2T1P	ENST00000641596.1	n.2194G>A		non_coding_transcript_exon_variant	2/2

Frequencies

GnomAD3 genomes AF: 0.185 AC: 28063 AN: 152026 Hom.: 2904 Cov.: 33

Gnomad AFR AF: 0.282

Gnomad AMI AF: 0.0330

Gnomad AMR AF: 0.168

Gnomad ASJ AF: 0.139

Gnomad EAS AF: 0.0892

Gnomad SAS AF: 0.171

Gnomad FIN AF: 0.138

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.150

Gnomad OTH AF: 0.176

GnomAD4 exome AF: 0.150 AC: 75 AN: 500 Hom.: 5 Cov.: 0 AF XY: 0.162 AC XY: 49 AN XY: 302

Gnomad4 FIN exome AF: 0.144

Gnomad4 NFE exome AF: 0.229

Gnomad4 OTH exome AF: 0.0625

GnomAD4 genome AF: 0.185 AC: 28089 AN: 152144 Hom.: 2907 Cov.: 33 AF XY: 0.182 AC XY: 13523 AN XY: 74406

Gnomad4 AFR AF: 0.281

Gnomad4 AMR AF: 0.168

Gnomad4 ASJ AF: 0.139

Gnomad4 EAS AF: 0.0892

Gnomad4 SAS AF: 0.172

Gnomad4 FIN AF: 0.138

Gnomad4 NFE AF: 0.150

Gnomad4 OTH AF: 0.174

Alfa AF: 0.154 Hom.: 1723

Bravo AF: 0.189

Asia WGS AF: 0.128 AC: 448 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	7.9
Dann	Benign	0.58

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: rs10405596; hg19: chr19-41314720; COSMIC: COSV58280250;