dbSNP rs1318743: ENSG00000251478:n.488A>G (chr5-41587300-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.488A>G variant causes a non coding transcript exon change. The variant allele was found at a frequency of 0.0451 in 424,716 control chromosomes in the GnomAD database, including 1,764 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 0.038 ( 466 hom., cov: 33)

Exomes 𝑓: 0.049 ( 1298 hom. )

Consequence

ENSG00000251478
ENST00000504215.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 3.74

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=-0.56).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.354 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TCP1P2		n.41587300T>C		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000251478	ENST00000504215.1 link	n.488A>G		non_coding_transcript_exon_variant	Exon 1 of 2	6
ENSG00000296840	ENST00000742936.1 link	n.105-241T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.0376

AC:

5724

AN:

152180

Hom.:

467

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0388

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0213

Gnomad ASJ

AF:

0.0184

Gnomad EAS

AF:

0.368

Gnomad SAS

AF:

0.144

Gnomad FIN

AF:

0.0103

Gnomad MID

AF:

0.0348

Gnomad NFE

AF:

0.0137

Gnomad OTH

AF:

0.0431

GnomAD4 exome

AF:

0.0493

AC:

13426

AN:

272418

Hom.:

1298

Cov.:

AF XY:

0.0550

AC XY:

8369

AN XY:

152142

show subpopulations

African (AFR)

AF:

0.0370

AC:

276

AN:

7456

American (AMR)

AF:

0.0122

AC:

223

AN:

18218

Ashkenazi Jewish (ASJ)

AF:

0.0196

AC:

124

AN:

6326

East Asian (EAS)

AF:

0.365

AC:

4322

AN:

11828

South Asian (SAS)

AF:

0.124

AC:

5587

AN:

44926

European-Finnish (FIN)

AF:

0.00899

AC:

154

AN:

17124

Middle Eastern (MID)

AF:

0.0464

AC:

AN:

1960

European-Non Finnish (NFE)

AF:

0.0139

AC:

2100

AN:

151270

Other (OTH)

AF:

0.0412

AC:

549

AN:

13310

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

500

1000

1500

2000

2500

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

140

280

420

560

700

<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:

0.0376

AC:

5719

AN:

152298

Hom.:

466

Cov.:

AF XY:

0.0405

AC XY:

3017

AN XY:

74466

show subpopulations

African (AFR)

AF:

0.0386

AC:

1607

AN:

41584

American (AMR)

AF:

0.0212

AC:

325

AN:

15302

Ashkenazi Jewish (ASJ)

AF:

0.0184

AC:

AN:

3472

East Asian (EAS)

AF:

0.367

AC:

1888

AN:

5138

South Asian (SAS)

AF:

0.143

AC:

691

AN:

4824

European-Finnish (FIN)

AF:

0.0103

AC:

110

AN:

10628

Middle Eastern (MID)

AF:

0.0306

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0137

AC:

929

AN:

68032

Other (OTH)

AF:

0.0455

AC:

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

259

519

778

1038

1297

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

148

222

296

370

<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:

0.0265

Hom.:

669

Bravo

AF:

0.0381

Asia WGS

AF:

0.236

AC:

822

AN:

3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.56

CADD

Benign

2.2

(source)

DANN

Benign

0.55

PhyloP100

3.7

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