rs41530251

Variant names:

• chr19-40810450-T-C
• rs41530251
• ENST00000601627.1:n.117+9035T>C

Your query was ambiguous. Multiple possible variants found:

• chr19-40810450-T-C
• chr19-40810450-T-G

Variant summary

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

The ENST00000601627.1(ENSG00000268797):​n.117+9035T>C variant causes a intron 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: ENSG00000268797 ENST00000601627.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.07
• Publications: 6 publications found

Genes affected

ENSG00000268797 (HGNC:):

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
CYP2T1P	NR_144551.1	n.562A>G		non_coding_transcript_exon_variant	Exon 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000268797	ENST00000601627.1	n.117+9035T>C		intron_variant	Intron 1 of 3	3		ENSP00000469533.1

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

GnomAD2 exomes AF: 0.405 AC: 54301 AN: 134164 AF XY: 0.404

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 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

African (AFR) AF: 0.104 AC: 895 AN: 8626

American (AMR) AF: 0.534 AC: 14549 AN: 27246

Ashkenazi Jewish (ASJ) AF: 0.311 AC: 3350 AN: 10778

East Asian (EAS) AF: 0.388 AC: 3570 AN: 9206

South Asian (SAS) AF: 0.413 AC: 24626 AN: 59658

European-Finnish (FIN) AF: 0.391 AC: 4995 AN: 12784

Middle Eastern (MID) AF: 0.296 AC: 818 AN: 2768

European-Non Finnish (NFE) AF: 0.400 AC: 63532 AN: 158906

Other (OTH) AF: 0.376 AC: 5356 AN: 14234

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

African (AFR) AF: 0.104 AC: 4330 AN: 41500

American (AMR) AF: 0.456 AC: 6958 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.321 AC: 1111 AN: 3466

East Asian (EAS) AF: 0.379 AC: 1945 AN: 5126

South Asian (SAS) AF: 0.413 AC: 1973 AN: 4782

European-Finnish (FIN) AF: 0.397 AC: 4190 AN: 10562

Middle Eastern (MID) AF: 0.299 AC: 88 AN: 294

European-Non Finnish (NFE) AF: 0.400 AC: 27133 AN: 67766

Other (OTH) AF: 0.359 AC: 759 AN: 2112

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
PhyloP100		4.1

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

Other links and lift over

dbSNP: rs41530251; hg19: chr19-41316355; COSMIC: COSV107337213;