rs6031869

Variant names:

• chr20-44932595-C-T
• rs6031869
• NM_001372179.1:c.1330+163C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001372179.1(PABPC1L):​c.1330+163C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.108 in 595,820 control chromosomes in the GnomAD database, including 4,535 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 (2118 hom., cov: 32)
  • Exomes 𝑓: 0.095 (2417 hom.)
• Consequence: PABPC1L NM_001372179.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.247
• Publications: 0 publications found

Genes affected

PABPC1L (HGNC:15797): (poly(A) binding protein cytoplasmic 1 like) This gene belongs to the polyadenylate-binding protein type-1 family of proteins. Members of this family bind to the polyA tails of mRNAs to regulate mRNA stability and translation. The mouse ortholog of this gene is required for female fertility. In human, expression of a functional protein is regulated by alternative splicing. The protein-coding splice variant for this gene is abundantly expressed in human oocytes, while a noncoding splice variant subject to nonsense-mediated decay is the predominant splice variant expressed in somatic tissues. [provided by RefSeq, Aug 2019]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.276 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001372179.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PABPC1L	NM_001372179.1	MANE Select	c.1330+163C>T		intron	N/A	NP_001359108.1
	PABPC1L	NR_134987.2		n.3134C>T		non_coding_transcript_exon	Exon 8 of 14
	PABPC1L	NR_134983.2		n.1266-477C>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PABPC1L	ENST00000217073.7	TSL:5 MANE Select	c.1330+163C>T		intron	N/A	ENSP00000217073.3
	PABPC1L	ENST00000537323.5	TSL:1	n.*189-477C>T		intron	N/A	ENSP00000445661.1
	PABPC1L	ENST00000372819.5	TSL:2	n.417C>T		non_coding_transcript_exon	Exon 1 of 6

Frequencies

GnomAD3 genomes AF: 0.143 AC: 21776 AN: 152008 Hom.: 2111 Cov.: 32

Gnomad AFR AF: 0.280

Gnomad AMI AF: 0.0593

Gnomad AMR AF: 0.0897

Gnomad ASJ AF: 0.112

Gnomad EAS AF: 0.138

Gnomad SAS AF: 0.0364

Gnomad FIN AF: 0.0934

Gnomad MID AF: 0.0701

Gnomad NFE AF: 0.0913

Gnomad OTH AF: 0.135

GnomAD4 exome AF: 0.0952 AC: 42241 AN: 443694 Hom.: 2417 Cov.: 6 AF XY: 0.0917 AC XY: 21157 AN XY: 230650

African (AFR) AF: 0.266 AC: 3200 AN: 12018

American (AMR) AF: 0.0762 AC: 1329 AN: 17452

Ashkenazi Jewish (ASJ) AF: 0.108 AC: 1407 AN: 13080

East Asian (EAS) AF: 0.139 AC: 4114 AN: 29660

South Asian (SAS) AF: 0.0397 AC: 1529 AN: 38466

European-Finnish (FIN) AF: 0.0897 AC: 2873 AN: 32042

Middle Eastern (MID) AF: 0.0899 AC: 175 AN: 1946

European-Non Finnish (NFE) AF: 0.0909 AC: 24875 AN: 273780

Other (OTH) AF: 0.108 AC: 2739 AN: 25250

GnomAD4 genome AF: 0.143 AC: 21812 AN: 152126 Hom.: 2118 Cov.: 32 AF XY: 0.141 AC XY: 10452 AN XY: 74384

African (AFR) AF: 0.280 AC: 11604 AN: 41456

American (AMR) AF: 0.0897 AC: 1372 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.112 AC: 390 AN: 3472

East Asian (EAS) AF: 0.137 AC: 711 AN: 5178

South Asian (SAS) AF: 0.0367 AC: 177 AN: 4826

European-Finnish (FIN) AF: 0.0934 AC: 988 AN: 10582

Middle Eastern (MID) AF: 0.0719 AC: 21 AN: 292

European-Non Finnish (NFE) AF: 0.0913 AC: 6209 AN: 68000

Other (OTH) AF: 0.136 AC: 286 AN: 2110

Alfa AF: 0.125 Hom.: 264

Bravo AF: 0.153

Asia WGS AF: 0.0870 AC: 305 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	7.8
DANN	Benign	0.84
PhyloP100		-0.25
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs6031869; hg19: chr20-43561236; COSMIC: COSV53840124; COSMIC: COSV53840124;