5-127512037-T-C

Position:

• chr5-127512037-T-C

Variant summary

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

The ENST00000510896.1(HNRNPKP1):​n.806A>G 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 0.321 in 1,225,712 control chromosomes in the GnomAD database, including 69,686 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 0.37 (12373 hom., cov: 31)
  • Exomes 𝑓: 0.31 (57313 hom.)
• Consequence: HNRNPKP1 ENST00000510896.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.42

Genes affected

HNRNPKP1 (HGNC:42374): (heterogeneous nuclear ribonucleoprotein K pseudogene 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.601 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
HNRNPKP1	ENST00000510896.1	n.806A>G		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.370 AC: 56209 AN: 151862 Hom.: 12324 Cov.: 31

Gnomad AFR AF: 0.584

Gnomad AMI AF: 0.136

Gnomad AMR AF: 0.372

Gnomad ASJ AF: 0.273

Gnomad EAS AF: 0.619

Gnomad SAS AF: 0.399

Gnomad FIN AF: 0.266

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.245

Gnomad OTH AF: 0.328

GnomAD4 exome AF: 0.314 AC: 336884 AN: 1073732 Hom.: 57313 Cov.: 18 AF XY: 0.311 AC XY: 170846 AN XY: 549266

Gnomad4 AFR exome AF: 0.613

Gnomad4 AMR exome AF: 0.441

Gnomad4 ASJ exome AF: 0.280

Gnomad4 EAS exome AF: 0.594

Gnomad4 SAS exome AF: 0.386

Gnomad4 FIN exome AF: 0.262

Gnomad4 NFE exome AF: 0.278

Gnomad4 OTH exome AF: 0.329

GnomAD4 genome AF: 0.370 AC: 56307 AN: 151980 Hom.: 12373 Cov.: 31 AF XY: 0.373 AC XY: 27710 AN XY: 74308

Gnomad4 AFR AF: 0.585

Gnomad4 AMR AF: 0.372

Gnomad4 ASJ AF: 0.273

Gnomad4 EAS AF: 0.619

Gnomad4 SAS AF: 0.399

Gnomad4 FIN AF: 0.266

Gnomad4 NFE AF: 0.245

Gnomad4 OTH AF: 0.323

Alfa AF: 0.265 Hom.: 7557

Bravo AF: 0.389

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	3.5
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs182844; hg19: chr5-126847729;