rs7949504

chr11-43130775-G-A

Variant summary

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

The ENST00000533565.1(HNRNPKP3):n.130-9375C>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 0.162 in 152,142 control chromosomes in the GnomAD database, including 2,141 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 (2141 hom., cov: 32)
• Consequence: HNRNPKP3 ENST00000533565.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.110

Genes affected

HNRNPKP3 (HGNC:42376): (heterogeneous nuclear ribonucleoprotein K pseudogene 3)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.184 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
HNRNPKP3	ENST00000533565.1	n.130-9375C>T		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.162 AC: 24612 AN: 152024 Hom.: 2141 Cov.: 32

Gnomad AFR AF: 0.134

Gnomad AMI AF: 0.125

Gnomad AMR AF: 0.131

Gnomad ASJ AF: 0.155

Gnomad EAS AF: 0.00232

Gnomad SAS AF: 0.133

Gnomad FIN AF: 0.257

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.187

Gnomad OTH AF: 0.162

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

GnomAD4 genome AF: 0.162 AC: 24624 AN: 152142 Hom.: 2141 Cov.: 32 AF XY: 0.162 AC XY: 12054 AN XY: 74356

Gnomad4 AFR AF: 0.134

Gnomad4 AMR AF: 0.130

Gnomad4 ASJ AF: 0.155

Gnomad4 EAS AF: 0.00233

Gnomad4 SAS AF: 0.132

Gnomad4 FIN AF: 0.257

Gnomad4 NFE AF: 0.186

Gnomad4 OTH AF: 0.163

Alfa AF: 0.175 Hom.: 1167

Bravo AF: 0.148

Asia WGS AF: 0.0770 AC: 266 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	3.3
Dann	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7949504; hg19: chr11-43152325;