chr4-134073497-T-C

Position:

• chr4-134073497-T-C

Variant summary

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

The ENST00000651116.1(ENSG00000286253):​n.351+10346T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.715 in 152,018 control chromosomes in the GnomAD database, including 39,407 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 0.71 (39407 hom., cov: 32)
• Consequence: ENSG00000286253 ENST00000651116.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.54

Genes affected

ENSG00000286253 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.926 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PABPC4L	XR_001741133.2	n.2163+29872A>G		intron_variant
PABPC4L	XR_001741134.2	n.1841+29872A>G		intron_variant
PABPC4L	XR_001741135.2	n.1841+29872A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000286253	ENST00000651116.1	n.351+10346T>C		intron_variant
ENSG00000251199	ENST00000658033.1	n.692+29872A>G		intron_variant
ENSG00000251199	ENST00000658435.1	n.560+29872A>G		intron_variant
ENSG00000251199	ENST00000668641.1	n.696+29872A>G		intron_variant

Frequencies

GnomAD3 genomes AF: 0.715 AC: 108597 AN: 151902 Hom.: 39370 Cov.: 32

Gnomad AFR AF: 0.785

Gnomad AMI AF: 0.760

Gnomad AMR AF: 0.710

Gnomad ASJ AF: 0.582

Gnomad EAS AF: 0.948

Gnomad SAS AF: 0.661

Gnomad FIN AF: 0.780

Gnomad MID AF: 0.557

Gnomad NFE AF: 0.658

Gnomad OTH AF: 0.652

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

GnomAD4 genome AF: 0.715 AC: 108685 AN: 152018 Hom.: 39407 Cov.: 32 AF XY: 0.722 AC XY: 53637 AN XY: 74304

Gnomad4 AFR AF: 0.785

Gnomad4 AMR AF: 0.710

Gnomad4 ASJ AF: 0.582

Gnomad4 EAS AF: 0.948

Gnomad4 SAS AF: 0.660

Gnomad4 FIN AF: 0.780

Gnomad4 NFE AF: 0.658

Gnomad4 OTH AF: 0.654

Alfa AF: 0.607 Hom.: 1793

Bravo AF: 0.712

Asia WGS AF: 0.779 AC: 2705 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.49
DANN	Benign	0.42

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;