dbSNP rs2297172: PTAR1:c.86+1423T>C (chr9-69758430-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_001099666.2(PTAR1):c.86+1423T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.144 in 152,338 control chromosomes in the GnomAD database, including 1,700 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 0.14 ( 1695 hom., cov: 31)

Exomes 𝑓: 0.12 ( 5 hom. )

Consequence

PTAR1
NM_001099666.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.343

Publications

5 publications found

Variant links:

Genes affected

PTAR1 (HGNC:30449): (protein prenyltransferase alpha subunit repeat containing 1) Predicted to enable protein prenyltransferase activity. Predicted to be involved in protein prenylation. Predicted to be active in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]

PTAR1 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=-0.87).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.253 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PTAR1	NM_001099666.2 link	c.86+1423T>C		intron_variant	Intron 1 of 7	ENST00000340434.5	NP_001093136.1	Q7Z6K3

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
PTAR1	ENST00000340434.5 link	c.86+1423T>C	intron_variant	Intron 1 of 7	1	NM_001099666.2	ENSP00000344299.4	Q7Z6K3
PTAR1	ENST00000377200.9 link	c.86+1423T>C	intron_variant	Intron 1 of 4	1		ENSP00000366405.5	X6R9N0
PTAR1	ENST00000472967.2 link	c.*271T>C	3_prime_UTR_variant	Exon 2 of 2	2		ENSP00000440164.1	F5GXY1
PTAR1	ENST00000474925.2 link	n.103+1423T>C	intron_variant	Intron 1 of 2	2

Frequencies

GnomAD3 genomes

AF:

0.144

AC:

21945

AN:

151932

Hom.:

1693

Cov.:

show subpopulations

Gnomad AFR

AF:

0.165

Gnomad AMI

AF:

0.0735

Gnomad AMR

AF:

0.133

Gnomad ASJ

AF:

0.206

Gnomad EAS

AF:

0.264

Gnomad SAS

AF:

0.167

Gnomad FIN

AF:

0.120

Gnomad MID

AF:

0.206

Gnomad NFE

AF:

0.125

Gnomad OTH

AF:

0.149

GnomAD4 exome

AF:

0.118

AC:

AN:

288

Hom.:

Cov.:

AF XY:

0.126

AC XY:

AN XY:

174

show subpopulations

African (AFR)

AF:

0.0714

AC:

AN:

American (AMR)

AF:

0.167

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.100

AC:

AN:

East Asian (EAS)

AF:

0.154

AC:

AN:

South Asian (SAS)

AF:

0.219

AC:

AN:

European-Finnish (FIN)

AF:

0.00

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.105

AC:

AN:

172

Other (OTH)

AF:

0.00

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.492

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<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:

0.144

AC:

21959

AN:

152050

Hom.:

1695

Cov.:

AF XY:

0.147

AC XY:

10898

AN XY:

74328

show subpopulations

African (AFR)

AF:

0.165

AC:

6852

AN:

41478

American (AMR)

AF:

0.133

AC:

2032

AN:

15268

Ashkenazi Jewish (ASJ)

AF:

0.206

AC:

716

AN:

3468

East Asian (EAS)

AF:

0.264

AC:

1368

AN:

5174

South Asian (SAS)

AF:

0.166

AC:

801

AN:

4816

European-Finnish (FIN)

AF:

0.120

AC:

1264

AN:

10538

Middle Eastern (MID)

AF:

0.207

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.125

AC:

8487

AN:

67992

Other (OTH)

AF:

0.147

AC:

311

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.495

Heterozygous variant carriers

897

1794

2692

3589

4486

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

234

468

702

936

1170

<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:

0.134

Hom.:

2384

Bravo

AF:

0.149

Asia WGS

AF:

0.182

AC:

637

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

9.6

(source)

DANN

Benign

0.60

PhyloP100

0.34

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

Details are displayed if max score is > 0.2

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