rs41530251

Positions:

• chr19-40810450-T-C

Variant summary

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

The NR_144551.1(CYP2T1P):​n.562A>G variant causes a non coding transcript exon change. The variant allele was found at a frequency of 0.374 in 455,984 control chromosomes in the GnomAD database, including 34,691 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 0.32 (9390 hom., cov: 32)
  • Exomes 𝑓: 0.40 (25301 hom.)
• Consequence: CYP2T1P NR_144551.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.07

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=-0.47).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.447 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CYP2T1P	NR_144551.1	n.562A>G		non_coding_transcript_exon_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CYP2T1P	ENST00000432607.2	n.531A>G		non_coding_transcript_exon_variant	4/9
CYP2T1P	ENST00000641596.1	n.559A>G		non_coding_transcript_exon_variant	2/2

Frequencies

GnomAD3 genomes AF: 0.322 AC: 48908 AN: 151660 Hom.: 9382 Cov.: 32

Gnomad AFR AF: 0.105

Gnomad AMI AF: 0.483

Gnomad AMR AF: 0.456

Gnomad ASJ AF: 0.321

Gnomad EAS AF: 0.379

Gnomad SAS AF: 0.412

Gnomad FIN AF: 0.397

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.400

Gnomad OTH AF: 0.355

GnomAD3 exomes AF: 0.405 AC: 54301 AN: 134164 Hom.: 11790 AF XY: 0.404 AC XY: 29559 AN XY: 73078

Gnomad AFR exome AF: 0.0957

Gnomad AMR exome AF: 0.534

Gnomad ASJ exome AF: 0.310

Gnomad EAS exome AF: 0.388

Gnomad SAS exome AF: 0.414

Gnomad FIN exome AF: 0.395

Gnomad NFE exome AF: 0.399

Gnomad OTH exome AF: 0.387

GnomAD4 exome AF: 0.400 AC: 121691 AN: 304206 Hom.: 25301 Cov.: 0 AF XY: 0.401 AC XY: 69467 AN XY: 173220

Gnomad4 AFR exome AF: 0.104

Gnomad4 AMR exome AF: 0.534

Gnomad4 ASJ exome AF: 0.311

Gnomad4 EAS exome AF: 0.388

Gnomad4 SAS exome AF: 0.413

Gnomad4 FIN exome AF: 0.391

Gnomad4 NFE exome AF: 0.400

Gnomad4 OTH exome AF: 0.376

GnomAD4 genome AF: 0.322 AC: 48924 AN: 151778 Hom.: 9390 Cov.: 32 AF XY: 0.326 AC XY: 24134 AN XY: 74140

Gnomad4 AFR AF: 0.104

Gnomad4 AMR AF: 0.456

Gnomad4 ASJ AF: 0.321

Gnomad4 EAS AF: 0.379

Gnomad4 SAS AF: 0.413

Gnomad4 FIN AF: 0.397

Gnomad4 NFE AF: 0.400

Gnomad4 OTH AF: 0.359

Alfa AF: 0.357 Hom.: 2427

Bravo AF: 0.318

Asia WGS AF: 0.415 AC: 1443 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.47
CADD	Benign	17
DANN	Benign	0.82

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: rs41530251; hg19: chr19-41316355;