rs1494978

chr4-134026646-G-A

Variant summary

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

The XR_001741133.2(PABPC4L):n.2164-15956C>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.357 in 151,818 control chromosomes in the GnomAD database, including 11,892 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 0.36 (11892 hom., cov: 32)
• Consequence: PABPC4L XR_001741133.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.104

Genes affected

PABPC4L (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.898 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PABPC4L	XR_001741133.2	n.2164-15956C>T		intron_variant, non_coding_transcript_variant
PABPC4L	XR_001741134.2	n.1842-15956C>T		intron_variant, non_coding_transcript_variant
PABPC4L	XR_001741135.2	n.1842-15956C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000658435.1			downstream_gene_variant
	ENST00000658033.1			downstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.357 AC: 54145 AN: 151700 Hom.: 11871 Cov.: 32

Gnomad AFR AF: 0.539

Gnomad AMI AF: 0.347

Gnomad AMR AF: 0.305

Gnomad ASJ AF: 0.285

Gnomad EAS AF: 0.920

Gnomad SAS AF: 0.393

Gnomad FIN AF: 0.268

Gnomad MID AF: 0.278

Gnomad NFE AF: 0.231

Gnomad OTH AF: 0.336

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

GnomAD4 genome AF: 0.357 AC: 54213 AN: 151818 Hom.: 11892 Cov.: 32 AF XY: 0.362 AC XY: 26842 AN XY: 74184

Gnomad4 AFR AF: 0.540

Gnomad4 AMR AF: 0.304

Gnomad4 ASJ AF: 0.285

Gnomad4 EAS AF: 0.920

Gnomad4 SAS AF: 0.392

Gnomad4 FIN AF: 0.268

Gnomad4 NFE AF: 0.231

Gnomad4 OTH AF: 0.342

Alfa AF: 0.259 Hom.: 7022

Bravo AF: 0.371

Asia WGS AF: 0.639 AC: 2217 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	1.8
Dann	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1494978; hg19: chr4-134947801;