Genetic Variant ENSG00000251478:n.200C>T (chr5-41587588-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000504215.1(ENSG00000251478):n.200C>T variant causes a non coding transcript exon change. The variant allele was found at a frequency of 0.0917 in 688,522 control chromosomes in the GnomAD database, including 4,541 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 0.10 ( 966 hom., cov: 33)

Exomes 𝑓: 0.088 ( 3575 hom. )

Consequence

ENSG00000251478
ENST00000504215.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 4.50

Publications

2 publications found

Variant links:

Genes affected

ENSG00000251478 (HGNC:):

ENSG00000251478 links:

TCP1P2 (HGNC:11660):

TCP1P2 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.65).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.174 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TCP1P2		n.41587588G>A		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000251478	ENST00000504215.1 link	n.200C>T		non_coding_transcript_exon_variant	Exon 1 of 2	6
ENSG00000296840	ENST00000742936.1 link	n.152G>A		non_coding_transcript_exon_variant	Exon 2 of 2

Frequencies

GnomAD3 genomes

AF:

0.103

AC:

15697

AN:

151998

Hom.:

964

Cov.:

show subpopulations

Gnomad AFR

AF:

0.178

Gnomad AMI

AF:

0.0451

Gnomad AMR

AF:

0.0845

Gnomad ASJ

AF:

0.120

Gnomad EAS

AF:

0.00407

Gnomad SAS

AF:

0.0635

Gnomad FIN

AF:

0.0507

Gnomad MID

AF:

0.136

Gnomad NFE

AF:

0.0802

Gnomad OTH

AF:

0.111

GnomAD4 exome

AF:

0.0884

AC:

47416

AN:

536406

Hom.:

3575

Cov.:

AF XY:

0.0877

AC XY:

25914

AN XY:

295470

show subpopulations

African (AFR)

AF:

0.196

AC:

3043

AN:

15492

American (AMR)

AF:

0.0854

AC:

3494

AN:

40898

Ashkenazi Jewish (ASJ)

AF:

0.136

AC:

2457

AN:

18114

East Asian (EAS)

AF:

0.00690

AC:

163

AN:

23614

South Asian (SAS)

AF:

0.0780

AC:

5377

AN:

68922

European-Finnish (FIN)

AF:

0.0591

AC:

2740

AN:

46396

Middle Eastern (MID)

AF:

0.132

AC:

277

AN:

2102

European-Non Finnish (NFE)

AF:

0.0922

AC:

27087

AN:

293680

Other (OTH)

AF:

0.102

AC:

2778

AN:

27188

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.591

Heterozygous variant carriers

1922

3843

5765

7686

9608

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

190

380

570

760

950

<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:

0.103

AC:

15700

AN:

152116

Hom.:

966

Cov.:

AF XY:

0.101

AC XY:

7479

AN XY:

74344

show subpopulations

African (AFR)

AF:

0.178

AC:

7371

AN:

41474

American (AMR)

AF:

0.0843

AC:

1289

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.120

AC:

416

AN:

3470

East Asian (EAS)

AF:

0.00408

AC:

AN:

5150

South Asian (SAS)

AF:

0.0627

AC:

302

AN:

4818

European-Finnish (FIN)

AF:

0.0507

AC:

536

AN:

10574

Middle Eastern (MID)

AF:

0.116

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0803

AC:

5459

AN:

68024

Other (OTH)

AF:

0.109

AC:

231

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

716

1433

2149

2866

3582

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

168

336

504

672

840

<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:

0.104

Hom.:

128

Bravo

AF:

0.110

Asia WGS

AF:

0.0500

AC:

174

AN:

3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.65

CADD

Benign

5.9

(source)

DANN

Benign

0.26

PhyloP100

4.5

Splicing

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