ENST00000510896.1:n.806A>G

Variant names:

• chr5-127512037-T-C
• rs182844
• ENST00000510896.1:n.806A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 6 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
HNRNPKP1		n.127512037T>C		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HNRNPKP1	ENST00000510896.1	n.806A>G		non_coding_transcript_exon_variant	Exon 1 of 1	6

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

African (AFR) AF: 0.613 AC: 16951 AN: 27666

American (AMR) AF: 0.441 AC: 18767 AN: 42532

Ashkenazi Jewish (ASJ) AF: 0.280 AC: 6323 AN: 22548

East Asian (EAS) AF: 0.594 AC: 22687 AN: 38216

South Asian (SAS) AF: 0.386 AC: 29574 AN: 76594

European-Finnish (FIN) AF: 0.262 AC: 13458 AN: 51452

Middle Eastern (MID) AF: 0.275 AC: 1355 AN: 4924

European-Non Finnish (NFE) AF: 0.278 AC: 212155 AN: 762372

Other (OTH) AF: 0.329 AC: 15614 AN: 47428

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

African (AFR) AF: 0.585 AC: 24220 AN: 41406

American (AMR) AF: 0.372 AC: 5691 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.273 AC: 947 AN: 3464

East Asian (EAS) AF: 0.619 AC: 3195 AN: 5160

South Asian (SAS) AF: 0.399 AC: 1916 AN: 4802

European-Finnish (FIN) AF: 0.266 AC: 2816 AN: 10582

Middle Eastern (MID) AF: 0.282 AC: 83 AN: 294

European-Non Finnish (NFE) AF: 0.245 AC: 16637 AN: 67976

Other (OTH) AF: 0.323 AC: 679 AN: 2102

Alfa AF: 0.277 Hom.: 10734

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
PhyloP100		2.4

Splicing

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

Other links and lift over

dbSNP: rs182844; hg19: chr5-126847729;