Genetic Variant ENST00000601627.1:n.117+9031A>G (chr19-40810444-A-G) – ACMG Classification: Likely_benign (-6 pts)

Variant summary

Our verdict is Likely benign. The variant received -6 ACMG points: 2P and 8B. PP3_ModerateBS1BS2

The ENST00000601627.1(ENSG00000268797):n.117+9029A>G variant causes a intron change. The variant allele was found at a frequency of 0.0217 in 456,042 control chromosomes in the GnomAD database, including 151 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 0.023 ( 39 hom., cov: 33)

Exomes 𝑓: 0.021 ( 112 hom. )

Consequence

ENSG00000268797
ENST00000601627.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 4.80

Publications

0 publications found

Variant links:

Genes affected

ENSG00000268797 (HGNC:):

ENSG00000268797 links:

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

CYP2T1P links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -6 ACMG points.

PP3

Splicing predictors support a deleterious effect. Scorers claiming Pathogenic: max_spliceai. No scorers claiming Uncertain. No scorers claiming Benign.

BS1

Variant frequency is greater than expected in population afr. GnomAd4 allele frequency = 0.0226 (3428/151888) while in subpopulation AFR AF = 0.0266 (1106/41524). AF 95% confidence interval is 0.0253. There are 39 homozygotes in GnomAd4. There are 1639 alleles in the male GnomAd4 subpopulation. Median coverage is 33. This position passed quality control check.

BS2

High Homozygotes in GnomAd4 at 39 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CYP2T1P	NR_144551.1 link	n.568T>C		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 link	n.117+9029A>G		intron_variant	Intron 1 of 3	3		ENSP00000469533.1		M0QY20

Frequencies

GnomAD3 genomes

AF:

0.0226

AC:

3428

AN:

151770

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0267

Gnomad AMI

AF:

0.0154

Gnomad AMR

AF:

0.0198

Gnomad ASJ

AF:

0.0283

Gnomad EAS

AF:

0.00425

Gnomad SAS

AF:

0.0182

Gnomad FIN

AF:

0.0144

Gnomad MID

AF:

0.0316

Gnomad NFE

AF:

0.0232

Gnomad OTH

AF:

0.0303

GnomAD2 exomes

AF:

0.0198

AC:

2656

AN:

134178

AF XY:

0.0198

show subpopulations

Gnomad AFR exome

AF:

0.0264

Gnomad AMR exome

AF:

0.0161

Gnomad ASJ exome

AF:

0.0311

Gnomad EAS exome

AF:

0.00381

Gnomad FIN exome

AF:

0.0165

Gnomad NFE exome

AF:

0.0225

Gnomad OTH exome

AF:

0.0242

GnomAD4 exome

AF:

0.0213

AC:

6484

AN:

304154

Hom.:

112

Cov.:

AF XY:

0.0208

AC XY:

3603

AN XY:

173186

show subpopulations

African (AFR)

AF:

0.0278

AC:

240

AN:

8622

American (AMR)

AF:

0.0174

AC:

474

AN:

27260

Ashkenazi Jewish (ASJ)

AF:

0.0313

AC:

337

AN:

10778

East Asian (EAS)

AF:

0.00500

AC:

AN:

9202

South Asian (SAS)

AF:

0.0193

AC:

1148

AN:

59590

European-Finnish (FIN)

AF:

0.0179

AC:

229

AN:

12790

Middle Eastern (MID)

AF:

0.0252

AC:

AN:

2776

European-Non Finnish (NFE)

AF:

0.0228

AC:

3623

AN:

158904

Other (OTH)

AF:

0.0223

AC:

317

AN:

14232

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.478

Heterozygous variant carriers

439

878

1318

1757

2196

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

104

130

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.0226

AC:

3428

AN:

151888

Hom.:

Cov.:

AF XY:

0.0221

AC XY:

1639

AN XY:

74236

show subpopulations

African (AFR)

AF:

0.0266

AC:

1106

AN:

41524

American (AMR)

AF:

0.0198

AC:

302

AN:

15264

Ashkenazi Jewish (ASJ)

AF:

0.0283

AC:

AN:

3458

East Asian (EAS)

AF:

0.00426

AC:

AN:

5168

South Asian (SAS)

AF:

0.0184

AC:

AN:

4770

European-Finnish (FIN)

AF:

0.0144

AC:

152

AN:

10580

Middle Eastern (MID)

AF:

0.0340

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0232

AC:

1573

AN:

67818

Other (OTH)

AF:

0.0300

AC:

AN:

2102

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.460

Heterozygous variant carriers

143

286

430

573

716

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

126

168

210

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0118

Hom.:

Bravo

AF:

0.0243

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.44

CADD

Benign

(source)

DANN

Benign

0.79

PhyloP100

4.8

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.82

Details are displayed if max score is > 0.2

DS_DG_spliceai

0.82

Position offset: -1

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over