rs10405596

Variant names:

• chr19-40808815-C-T
• rs10405596
• ENST00000601627.1:n.117+7400C>T

Variant summary

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

The ENST00000601627.1(ENSG00000268797):​n.117+7400C>T variant causes a intron 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: ENSG00000268797 ENST00000601627.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.305
• Publications: 7 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=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.277 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000601627.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CYP2T1P	NR_144551.1		n.2197G>A		non_coding_transcript_exon	Exon 2 of 2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000268797	ENST00000601627.1	TSL:3	n.117+7400C>T		intron	N/A	ENSP00000469533.1
	CYP2T1P	ENST00000432607.2	TSL:6	n.1246G>A		non_coding_transcript_exon	Exon 8 of 9
	CYP2T1P	ENST00000641596.2		n.2194G>A		non_coding_transcript_exon	Exon 2 of 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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.144 AC: 63 AN: 436

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.229 AC: 11 AN: 48

Other (OTH) AF: 0.0625 AC: 1 AN: 16

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

African (AFR) AF: 0.281 AC: 11659 AN: 41478

American (AMR) AF: 0.168 AC: 2570 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.139 AC: 481 AN: 3472

East Asian (EAS) AF: 0.0892 AC: 462 AN: 5178

South Asian (SAS) AF: 0.172 AC: 831 AN: 4826

European-Finnish (FIN) AF: 0.138 AC: 1462 AN: 10602

Middle Eastern (MID) AF: 0.167 AC: 49 AN: 294

European-Non Finnish (NFE) AF: 0.150 AC: 10177 AN: 67974

Other (OTH) AF: 0.174 AC: 368 AN: 2114

Alfa AF: 0.165 Hom.: 5501

Bravo AF: 0.189

Asia WGS AF: 0.128 AC: 448 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	7.9
DANN	Benign	0.58
PhyloP100		-0.30

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