9-69758430-A-G

Position:

• chr9-69758430-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.343

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]

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
PTAR1	NM_001099666.2	c.86+1423T>C		intron_variant		ENST00000340434.5	NP_001093136.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PTAR1	ENST00000340434.5	c.86+1423T>C		intron_variant		1	NM_001099666.2	ENSP00000344299	P1
PTAR1	ENST00000377200.9	c.86+1423T>C		intron_variant		1		ENSP00000366405
PTAR1	ENST00000472967.2	c.*271T>C		3_prime_UTR_variant	2/2	2		ENSP00000440164
PTAR1	ENST00000474925.2	n.103+1423T>C		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.144 AC: 21945 AN: 151932 Hom.: 1693 Cov.: 31

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: 34 AN: 288 Hom.: 5 Cov.: 0 AF XY: 0.126 AC XY: 22 AN XY: 174

Gnomad4 AFR exome AF: 0.0714

Gnomad4 AMR exome AF: 0.167

Gnomad4 ASJ exome AF: 0.100

Gnomad4 EAS exome AF: 0.154

Gnomad4 SAS exome AF: 0.219

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.105

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.144 AC: 21959 AN: 152050 Hom.: 1695 Cov.: 31 AF XY: 0.147 AC XY: 10898 AN XY: 74328

Gnomad4 AFR AF: 0.165

Gnomad4 AMR AF: 0.133

Gnomad4 ASJ AF: 0.206

Gnomad4 EAS AF: 0.264

Gnomad4 SAS AF: 0.166

Gnomad4 FIN AF: 0.120

Gnomad4 NFE AF: 0.125

Gnomad4 OTH AF: 0.147

Alfa AF: 0.133 Hom.: 1867

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
DANN	Benign	0.60

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

LitVar

Other links and lift over

dbSNP: rs2297172; hg19: chr9-72373346;