15-44711166-T-G

Variant summary

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

The NM_001387263.1(PATL2):c.-400A>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 0.847 in 410,114 control chromosomes in the GnomAD database, including 148,442 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 0.82 (51567 hom., cov: 30)
  • Exomes 𝑓: 0.86 (96875 hom.)
• Consequence: PATL2 NM_001387263.1 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.14

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=-0.78).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.883 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PATL2	NM_001387263.1	c.-400A>C		5_prime_UTR_variant	1/18	ENST00000682850.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PATL2	ENST00000682850.1	c.-400A>C		5_prime_UTR_variant	1/18		NM_001387263.1	A2
PATL2	ENST00000558573.1	n.151A>C		non_coding_transcript_exon_variant	1/2	2

Frequencies

GnomAD3 genomes AF: 0.817 AC: 124166 AN: 151940 Hom.: 51539 Cov.: 30

Gnomad AFR AF: 0.657

Gnomad AMI AF: 0.918

Gnomad AMR AF: 0.880

Gnomad ASJ AF: 0.848

Gnomad EAS AF: 0.841

Gnomad SAS AF: 0.784

Gnomad FIN AF: 0.868

Gnomad MID AF: 0.902

Gnomad NFE AF: 0.889

Gnomad OTH AF: 0.835

GnomAD4 exome AF: 0.864 AC: 222927 AN: 258056 Hom.: 96875 Cov.: 0 AF XY: 0.859 AC XY: 117012 AN XY: 136170

Gnomad4 AFR exome AF: 0.654

Gnomad4 AMR exome AF: 0.887

Gnomad4 ASJ exome AF: 0.843

Gnomad4 EAS exome AF: 0.872

Gnomad4 SAS exome AF: 0.802

Gnomad4 FIN exome AF: 0.867

Gnomad4 NFE exome AF: 0.889

Gnomad4 OTH exome AF: 0.853

GnomAD4 genome AF: 0.817 AC: 124241 AN: 152058 Hom.: 51567 Cov.: 30 AF XY: 0.817 AC XY: 60711 AN XY: 74294

Gnomad4 AFR AF: 0.657

Gnomad4 AMR AF: 0.881

Gnomad4 ASJ AF: 0.848

Gnomad4 EAS AF: 0.842

Gnomad4 SAS AF: 0.785

Gnomad4 FIN AF: 0.868

Gnomad4 NFE AF: 0.889

Gnomad4 OTH AF: 0.832

Alfa AF: 0.880 Hom.: 86289

Bravo AF: 0.811

Asia WGS AF: 0.745 AC: 2592 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
Cadd	Benign	2.9
Dann	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2255235; hg19: chr15-45003364; COSMIC: COSV62564956;