Genetic Variant ENSG00000251478:n.1141A>G (chr5-41586303-T-C) – 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.1141A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.389 in 506,432 control chromosomes in the GnomAD database, including 40,421 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 0.41 ( 13419 hom., cov: 32)

Exomes 𝑓: 0.38 ( 27002 hom. )

Consequence

ENSG00000251478
ENST00000504215.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.04

Publications

3 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=-0.68).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.54 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TCP1P2		n.41586303T>C		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000251478	ENST00000504215.1 link	n.1141A>G		non_coding_transcript_exon_variant	Exon 2 of 2	6
ENSG00000296840	ENST00000742936.1 link	n.105-1238T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.409

AC:

62089

AN:

151862

Hom.:

13415

Cov.:

show subpopulations

Gnomad AFR

AF:

0.546

Gnomad AMI

AF:

0.516

Gnomad AMR

AF:

0.324

Gnomad ASJ

AF:

0.484

Gnomad EAS

AF:

0.449

Gnomad SAS

AF:

0.510

Gnomad FIN

AF:

0.278

Gnomad MID

AF:

0.487

Gnomad NFE

AF:

0.348

Gnomad OTH

AF:

0.426

GnomAD4 exome

AF:

0.380

AC:

134816

AN:

354452

Hom.:

27002

Cov.:

AF XY:

0.389

AC XY:

73460

AN XY:

188622

show subpopulations

African (AFR)

AF:

0.550

AC:

5726

AN:

10414

American (AMR)

AF:

0.272

AC:

4133

AN:

15188

Ashkenazi Jewish (ASJ)

AF:

0.510

AC:

5430

AN:

10652

East Asian (EAS)

AF:

0.428

AC:

9593

AN:

22434

South Asian (SAS)

AF:

0.509

AC:

20845

AN:

40972

European-Finnish (FIN)

AF:

0.296

AC:

7259

AN:

24538

Middle Eastern (MID)

AF:

0.507

AC:

747

AN:

1472

European-Non Finnish (NFE)

AF:

0.351

AC:

73246

AN:

208824

Other (OTH)

AF:

0.393

AC:

7837

AN:

19958

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.510

Heterozygous variant carriers

3800

7600

11399

15199

18999

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

500

1000

1500

2000

2500

<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:

0.409

AC:

62118

AN:

151980

Hom.:

13419

Cov.:

AF XY:

0.408

AC XY:

30281

AN XY:

74290

show subpopulations

African (AFR)

AF:

0.546

AC:

22634

AN:

41442

American (AMR)

AF:

0.324

AC:

4944

AN:

15278

Ashkenazi Jewish (ASJ)

AF:

0.484

AC:

1678

AN:

3470

East Asian (EAS)

AF:

0.449

AC:

2303

AN:

5134

South Asian (SAS)

AF:

0.509

AC:

2448

AN:

4812

European-Finnish (FIN)

AF:

0.278

AC:

2938

AN:

10580

Middle Eastern (MID)

AF:

0.473

AC:

139

AN:

294

European-Non Finnish (NFE)

AF:

0.348

AC:

23672

AN:

67952

Other (OTH)

AF:

0.423

AC:

891

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1816

3633

5449

7266

9082

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

580

1160

1740

2320

2900

<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:

0.373

Hom.:

32781

Bravo

AF:

0.415

Asia WGS

AF:

0.497

AC:

1727

AN:

3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.68

CADD

Benign

2.0

(source)

DANN

Benign

0.32

PhyloP100

2.0

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