chr4-134073497-T-C

Variant names:

• chr4-134073497-T-C
• rs2220875
• ENST00000651116.1:n.351+10346T>C

Variant summary

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

The ENST00000651116.1(ENSG00000286253):​n.351+10346T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.715 in 152,018 control chromosomes in the GnomAD database, including 39,407 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 0.71 (39407 hom., cov: 32)
• Consequence: ENSG00000286253 ENST00000651116.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.54
• Publications: 1 publications found

Genes affected

ENSG00000286253 (HGNC:):

PABPC4L (HGNC:31955): (poly(A) binding protein cytoplasmic 4 like) Predicted to enable mRNA 3'-UTR binding activity; poly(A) binding activity; and poly(U) RNA binding activity. Predicted to be part of ribonucleoprotein complex. Predicted to be active in cytoplasmic stress granule; cytosol; and nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -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 = 0.926 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000651116.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000286253	ENST00000651116.1		n.351+10346T>C		intron	N/A
	ENSG00000251199	ENST00000658033.2		n.726+29872A>G		intron	N/A
	ENSG00000251199	ENST00000658435.1		n.560+29872A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.715 AC: 108597 AN: 151902 Hom.: 39370 Cov.: 32

Gnomad AFR AF: 0.785

Gnomad AMI AF: 0.760

Gnomad AMR AF: 0.710

Gnomad ASJ AF: 0.582

Gnomad EAS AF: 0.948

Gnomad SAS AF: 0.661

Gnomad FIN AF: 0.780

Gnomad MID AF: 0.557

Gnomad NFE AF: 0.658

Gnomad OTH AF: 0.652

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

GnomAD4 genome AF: 0.715 AC: 108685 AN: 152018 Hom.: 39407 Cov.: 32 AF XY: 0.722 AC XY: 53637 AN XY: 74304

African (AFR) AF: 0.785 AC: 32561 AN: 41488

American (AMR) AF: 0.710 AC: 10834 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.582 AC: 2018 AN: 3470

East Asian (EAS) AF: 0.948 AC: 4868 AN: 5134

South Asian (SAS) AF: 0.660 AC: 3185 AN: 4824

European-Finnish (FIN) AF: 0.780 AC: 8255 AN: 10590

Middle Eastern (MID) AF: 0.551 AC: 162 AN: 294

European-Non Finnish (NFE) AF: 0.658 AC: 44731 AN: 67948

Other (OTH) AF: 0.654 AC: 1378 AN: 2106

Alfa AF: 0.621 Hom.: 2023

Bravo AF: 0.712

Asia WGS AF: 0.779 AC: 2705 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.49
DANN	Benign	0.42
PhyloP100		-2.5

Splicing

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

Other links and lift over

dbSNP: rs2220875; hg19: chr4-134994652;