rs2220875

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr4-134073497-T-A
• chr4-134073497-T-C
• chr4-134073497-T-G

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000651116.1(ENSG00000286253):​n.351+10346T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
• Consequence: ENSG00000286253 ENST00000651116.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.54

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

Verdict is Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PABPC4L	XR_001741133.2	n.2163+29872A>T		intron_variant	Intron 3 of 7
PABPC4L	XR_001741134.2	n.1841+29872A>T		intron_variant	Intron 3 of 8
PABPC4L	XR_001741135.2	n.1841+29872A>T		intron_variant	Intron 3 of 7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000286253	ENST00000651116.1	n.351+10346T>A		intron_variant	Intron 2 of 2
ENSG00000251199	ENST00000658033.1	n.692+29872A>T		intron_variant	Intron 4 of 4
ENSG00000251199	ENST00000658435.1	n.560+29872A>T		intron_variant	Intron 3 of 3
ENSG00000251199	ENST00000668641.1	n.696+29872A>T		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes Cov.: 32

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

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.39
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2220875; hg19: chr4-134994652;