rs16966334

chr15-44710916-C-G

Variant summary

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

The NM_001387263.1(PATL2):c.-240G>C variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0539 in 151,598 control chromosomes in the GnomAD database, including 384 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 0.054 (359 hom., cov: 29)
  • Exomes 𝑓: 0.058 (25 hom.)
• Consequence: PATL2 NM_001387263.1 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.301

Genes affected

PATL2 (HGNC:33630): (PAT1 homolog 2) Predicted to enable RNA binding activity. Predicted to be involved in P-body assembly and deadenylation-dependent decapping of nuclear-transcribed mRNA. Predicted to act upstream of or within negative regulation of cytoplasmic mRNA processing body assembly. Located 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=-0.74).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.175 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PATL2	NM_001387263.1	c.-240G>C		5_prime_UTR_variant	2/18	ENST00000682850.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PATL2	ENST00000682850.1	c.-240G>C		5_prime_UTR_variant	2/18		NM_001387263.1	A2
PATL2	ENST00000558573.1	n.297+104G>C		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.0537 AC: 7841 AN: 146064 Hom.: 361 Cov.: 29

Gnomad AFR AF: 0.0782

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.105

Gnomad ASJ AF: 0.0297

Gnomad EAS AF: 0.186

Gnomad SAS AF: 0.126

Gnomad FIN AF: 0.0122

Gnomad MID AF: 0.00347

Gnomad NFE AF: 0.0221

Gnomad OTH AF: 0.0465

GnomAD4 exome AF: 0.0578 AC: 314 AN: 5428 Hom.: 25 AF XY: 0.0631 AC XY: 194 AN XY: 3074

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.117

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.133

Gnomad4 SAS exome AF: 0.0817

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.0161

Gnomad4 OTH exome AF: 0.0309

GnomAD4 genome AF: 0.0537 AC: 7853 AN: 146170 Hom.: 359 Cov.: 29 AF XY: 0.0551 AC XY: 3892 AN XY: 70692

Gnomad4 AFR AF: 0.0783

Gnomad4 AMR AF: 0.106

Gnomad4 ASJ AF: 0.0297

Gnomad4 EAS AF: 0.186

Gnomad4 SAS AF: 0.124

Gnomad4 FIN AF: 0.0122

Gnomad4 NFE AF: 0.0221

Gnomad4 OTH AF: 0.0475

Alfa AF: 0.0410 Hom.: 22

Bravo AF: 0.0615

Asia WGS AF: 0.135 AC: 468 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
Cadd	Benign	5.7
Dann	Benign	0.75

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs16966334; hg19: chr15-45003114;