rs13096522

Positions:

• chr3-96350694-T-A

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000485383.1(HNRNPKP4):​n.1141T>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.196 in 1,201,736 control chromosomes in the GnomAD database, including 24,911 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 0.16 (2524 hom., cov: 32)
  • Exomes 𝑓: 0.20 (22387 hom.)
• Consequence: HNRNPKP4 ENST00000485383.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.179

Genes affected

HNRNPKP4 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.44).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.24 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
HNRNPKP4		n.96350694T>A		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
HNRNPKP4	ENST00000485383.1	n.1141T>A		non_coding_transcript_exon_variant	1/1	6

Frequencies

GnomAD3 genomes AF: 0.159 AC: 24217 AN: 151996 Hom.: 2527 Cov.: 32

Gnomad AFR AF: 0.0382

Gnomad AMI AF: 0.249

Gnomad AMR AF: 0.175

Gnomad ASJ AF: 0.179

Gnomad EAS AF: 0.251

Gnomad SAS AF: 0.190

Gnomad FIN AF: 0.286

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.199

Gnomad OTH AF: 0.152

GnomAD4 exome AF: 0.202 AC: 211864 AN: 1049622 Hom.: 22387 Cov.: 15 AF XY: 0.201 AC XY: 108678 AN XY: 541552

Gnomad4 AFR exome AF: 0.0370

Gnomad4 AMR exome AF: 0.198

Gnomad4 ASJ exome AF: 0.185

Gnomad4 EAS exome AF: 0.252

Gnomad4 SAS exome AF: 0.186

Gnomad4 FIN exome AF: 0.273

Gnomad4 NFE exome AF: 0.203

Gnomad4 OTH exome AF: 0.192

GnomAD4 genome AF: 0.159 AC: 24206 AN: 152114 Hom.: 2524 Cov.: 32 AF XY: 0.162 AC XY: 12070 AN XY: 74342

Gnomad4 AFR AF: 0.0381

Gnomad4 AMR AF: 0.175

Gnomad4 ASJ AF: 0.179

Gnomad4 EAS AF: 0.251

Gnomad4 SAS AF: 0.188

Gnomad4 FIN AF: 0.286

Gnomad4 NFE AF: 0.199

Gnomad4 OTH AF: 0.151

Alfa AF: 0.187 Hom.: 393

Bravo AF: 0.147

Asia WGS AF: 0.253 AC: 879 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.44
CADD	Benign	7.7
DANN	Benign	0.86

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13096522; hg19: chr3-96069538;