rs1494978

Variant names:

• chr4-134026646-G-A
• rs1494978
• ENST00000736140.1:n.212-15956C>T

Your query was ambiguous. Multiple possible variants found:

• chr4-134026646-G-A
• chr4-134026646-G-C
• chr4-134026646-G-T

Variant summary

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

The ENST00000736140.1(ENSG00000251388):​n.212-15956C>T variant causes a intron 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: ENSG00000251388 ENST00000736140.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.104
• Publications: 4 publications found

Genes affected

ENSG00000251388 (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=-0.95).
• 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 rank	MANE	Protein	UniProt
PABPC4L	XR_001741133.2	n.2164-15956C>T		intron_variant	Intron 3 of 7
PABPC4L	XR_001741134.2	n.1842-15956C>T		intron_variant	Intron 3 of 8
PABPC4L	XR_001741135.2	n.1842-15956C>T		intron_variant	Intron 3 of 7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000251388	ENST00000736140.1	n.212-15956C>T		intron_variant	Intron 1 of 4
ENSG00000251199	ENST00000658033.2	n.*16C>T		downstream_gene_variant
ENSG00000251199	ENST00000658435.1	n.*19C>T		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

African (AFR) AF: 0.540 AC: 22338 AN: 41388

American (AMR) AF: 0.304 AC: 4629 AN: 15214

Ashkenazi Jewish (ASJ) AF: 0.285 AC: 988 AN: 3466

East Asian (EAS) AF: 0.920 AC: 4749 AN: 5164

South Asian (SAS) AF: 0.392 AC: 1885 AN: 4812

European-Finnish (FIN) AF: 0.268 AC: 2821 AN: 10516

Middle Eastern (MID) AF: 0.286 AC: 84 AN: 294

European-Non Finnish (NFE) AF: 0.231 AC: 15683 AN: 67950

Other (OTH) AF: 0.342 AC: 720 AN: 2104

Alfa AF: 0.268 Hom.: 9850

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
PhyloP100		-0.10

Splicing

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

Other links and lift over

dbSNP: rs1494978; hg19: chr4-134947801;