dbSNP rs1928313: THAP3P1:n.923-14103C>T (chr1-104111459-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000634580.1(THAP3P1):n.923-14103C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0434 in 152,210 control chromosomes in the GnomAD database, including 303 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 0.043 ( 303 hom., cov: 32)

Consequence

THAP3P1
ENST00000634580.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.409

Publications

3 publications found

Variant links:

Genes affected

THAP3P1 (HGNC:):

THAP3P1 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=-1.04).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.112 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
THAP3P1	ENST00000634580.1 link	n.923-14103C>T	intron_variant	Intron 1 of 1	5
THAP3P1	ENST00000634888.1 link	n.735+37555C>T	intron_variant	Intron 1 of 3	5
THAP3P1	ENST00000634997.1 link	n.252-14103C>T	intron_variant	Intron 2 of 2	4

Frequencies

GnomAD3 genomes

AF:

0.0432

AC:

6577

AN:

152092

Hom.:

301

Cov.:

show subpopulations

Gnomad AFR

AF:

0.114

Gnomad AMI

AF:

0.0263

Gnomad AMR

AF:

0.0252

Gnomad ASJ

AF:

0.0268

Gnomad EAS

AF:

0.0168

Gnomad SAS

AF:

0.0339

Gnomad FIN

AF:

0.00933

Gnomad MID

AF:

0.0348

Gnomad NFE

AF:

0.0134

Gnomad OTH

AF:

0.0407

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.0434

AC:

6605

AN:

152210

Hom.:

303

Cov.:

AF XY:

0.0439

AC XY:

3268

AN XY:

74422

show subpopulations

African (AFR)

AF:

0.114

AC:

4748

AN:

41528

American (AMR)

AF:

0.0251

AC:

383

AN:

15276

Ashkenazi Jewish (ASJ)

AF:

0.0268

AC:

AN:

3472

East Asian (EAS)

AF:

0.0168

AC:

AN:

5170

South Asian (SAS)

AF:

0.0344

AC:

166

AN:

4828

European-Finnish (FIN)

AF:

0.00933

AC:

AN:

10614

Middle Eastern (MID)

AF:

0.0374

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0134

AC:

909

AN:

68004

Other (OTH)

AF:

0.0402

AC:

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

304

608

913

1217

1521

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

152

228

304

380

<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:

0.0289

Hom.:

Bravo

AF:

0.0481

Asia WGS

AF:

0.0330

AC:

114

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

0.77

(source)

DANN

Benign

0.23

PhyloP100

-0.41

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

ClinVar

Computational scores

Splicing

Publications

Other links and lift over