rs12365397

Variant names:

• chr11-43214511-A-G
• rs12365397
• ENST00000533565.1:n.129+54754T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000533565.1(HNRNPKP3):​n.129+54754T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.238 in 152,106 control chromosomes in the GnomAD database, including 5,124 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 0.24 (5124 hom., cov: 32)
• Consequence: HNRNPKP3 ENST00000533565.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0190
• Publications: 5 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.31 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HNRNPKP3	ENST00000533565.1	n.129+54754T>C		intron_variant	Intron 1 of 2	4
HNRNPKP3	ENST00000770296.1	n.186+54754T>C		intron_variant	Intron 1 of 2
HNRNPKP3	ENST00000770297.1	n.115-36520T>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.238 AC: 36213 AN: 151988 Hom.: 5122 Cov.: 32

Gnomad AFR AF: 0.0941

Gnomad AMI AF: 0.475

Gnomad AMR AF: 0.206

Gnomad ASJ AF: 0.248

Gnomad EAS AF: 0.239

Gnomad SAS AF: 0.279

Gnomad FIN AF: 0.331

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.313

Gnomad OTH AF: 0.220

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

GnomAD4 genome AF: 0.238 AC: 36218 AN: 152106 Hom.: 5124 Cov.: 32 AF XY: 0.239 AC XY: 17766 AN XY: 74368

African (AFR) AF: 0.0939 AC: 3897 AN: 41512

American (AMR) AF: 0.205 AC: 3138 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.248 AC: 860 AN: 3468

East Asian (EAS) AF: 0.239 AC: 1234 AN: 5166

South Asian (SAS) AF: 0.279 AC: 1347 AN: 4820

European-Finnish (FIN) AF: 0.331 AC: 3498 AN: 10574

Middle Eastern (MID) AF: 0.218 AC: 64 AN: 294

European-Non Finnish (NFE) AF: 0.313 AC: 21287 AN: 67968

Other (OTH) AF: 0.218 AC: 461 AN: 2114

Alfa AF: 0.287 Hom.: 28506

Bravo AF: 0.221

Asia WGS AF: 0.212 AC: 741 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.88
DANN	Benign	0.58
PhyloP100		0.019

Splicing

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

Other links and lift over

dbSNP: rs12365397; hg19: chr11-43236061;