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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000736140.1. 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
	ENSG00000251388	ENST00000736140.1		n.212-15956C>T		intron	N/A
	ENSG00000251199	ENST00000658033.2		n.*16C>T		downstream_gene	N/A
	ENSG00000251199	ENST00000658435.1		n.*19C>T		downstream_gene	N/A

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1494978;

hg19: chr4-134947801;