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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001099666.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
PTAR1	NM_001099666.2	MANE Select	c.86+1423T>C	intron	N/A	NP_001093136.1	Q7Z6K3
PTAR1	NM_001366936.1		c.86+1423T>C	intron	N/A	NP_001353865.1
PTAR1	NM_001366937.1		c.86+1423T>C	intron	N/A	NP_001353866.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
PTAR1	ENST00000340434.5	TSL:1 MANE Select	c.86+1423T>C	intron	N/A	ENSP00000344299.4	Q7Z6K3
PTAR1	ENST00000377200.9	TSL:1	c.86+1423T>C	intron	N/A	ENSP00000366405.5	X6R9N0
PTAR1	ENST00000472967.2	TSL:2	c.*271T>C	3_prime_UTR	Exon 2 of 2	ENSP00000440164.1	F5GXY1

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 v4.9

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over