rs3758872

Positions:

• chr11-59653702-G-C

Variant summary

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

The NM_152716.3(PATL1):​c.1121+281C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.11 in 152,136 control chromosomes in the GnomAD database, including 1,144 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 0.11 (1144 hom., cov: 32)
• Consequence: PATL1 NM_152716.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.414

Genes affected

PATL1 (HGNC:26721): (PAT1 homolog 1, processing body mRNA decay factor) Enables poly(G) binding activity and poly(U) RNA binding activity. Involved in P-body assembly and deadenylation-dependent decapping of nuclear-transcribed mRNA. Located in P-body and cytosol. Colocalizes with CCR4-NOT complex. [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=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.173 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PATL1	NM_152716.3	c.1121+281C>G		intron_variant		ENST00000300146.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PATL1	ENST00000300146.10	c.1121+281C>G		intron_variant		1	NM_152716.3	P1

Frequencies

GnomAD3 genomes AF: 0.110 AC: 16744 AN: 152018 Hom.: 1138 Cov.: 32

Gnomad AFR AF: 0.0295

Gnomad AMI AF: 0.126

Gnomad AMR AF: 0.102

Gnomad ASJ AF: 0.114

Gnomad EAS AF: 0.183

Gnomad SAS AF: 0.119

Gnomad FIN AF: 0.156

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.147

Gnomad OTH AF: 0.103

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.110 AC: 16759 AN: 152136 Hom.: 1144 Cov.: 32 AF XY: 0.111 AC XY: 8226 AN XY: 74368

Gnomad4 AFR AF: 0.0295

Gnomad4 AMR AF: 0.102

Gnomad4 ASJ AF: 0.114

Gnomad4 EAS AF: 0.182

Gnomad4 SAS AF: 0.120

Gnomad4 FIN AF: 0.156

Gnomad4 NFE AF: 0.147

Gnomad4 OTH AF: 0.107

Alfa AF: 0.122 Hom.: 164

Bravo AF: 0.104

Asia WGS AF: 0.143 AC: 498 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	2.5
DANN	Benign	0.79

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		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: rs3758872; hg19: chr11-59421175;