5-127512037-T-C

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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000510896.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HNRNPKP1	ENST00000510896.1	TSL:6	n.806A>G		non_coding_transcript_exon	Exon 1 of 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

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 v4.9

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;