4-134141580-T-G

Variant names:

• chr4-134141580-T-G
• rs3980965
• ENST00000654404.1:n.979+668A>C

Variant summary

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

The ENST00000654404.1(ENSG00000251199):​n.979+668A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.485 in 150,898 control chromosomes in the GnomAD database, including 21,293 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 0.48 (21293 hom., cov: 32)
• Consequence: ENSG00000251199 ENST00000654404.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.50
• Publications: 3 publications found

Genes affected

ENSG00000251199 (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=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.937 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000654404.1. 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
	ENSG00000251199	ENST00000654404.1		n.979+668A>C		intron	N/A
	ENSG00000251199	ENST00000658033.2		n.577+24906A>C		intron	N/A
	ENSG00000251199	ENST00000658435.1		n.412-38063A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.485 AC: 73083 AN: 150806 Hom.: 21249 Cov.: 32

Gnomad AFR AF: 0.756

Gnomad AMI AF: 0.425

Gnomad AMR AF: 0.503

Gnomad ASJ AF: 0.409

Gnomad EAS AF: 0.959

Gnomad SAS AF: 0.527

Gnomad FIN AF: 0.341

Gnomad MID AF: 0.382

Gnomad NFE AF: 0.304

Gnomad OTH AF: 0.469

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

GnomAD4 genome AF: 0.485 AC: 73176 AN: 150898 Hom.: 21293 Cov.: 32 AF XY: 0.492 AC XY: 36250 AN XY: 73682

African (AFR) AF: 0.756 AC: 31206 AN: 41270

American (AMR) AF: 0.504 AC: 7589 AN: 15072

Ashkenazi Jewish (ASJ) AF: 0.409 AC: 1413 AN: 3458

East Asian (EAS) AF: 0.960 AC: 4928 AN: 5136

South Asian (SAS) AF: 0.526 AC: 2533 AN: 4818

European-Finnish (FIN) AF: 0.341 AC: 3520 AN: 10336

Middle Eastern (MID) AF: 0.384 AC: 112 AN: 292

European-Non Finnish (NFE) AF: 0.304 AC: 20496 AN: 67512

Other (OTH) AF: 0.474 AC: 991 AN: 2092

Alfa AF: 0.340 Hom.: 11055

Bravo AF: 0.510

Asia WGS AF: 0.784 AC: 2713 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.17
DANN	Benign	0.50
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs3980965; hg19: chr4-135062735;