rs7119153

Variant names:

• chr11-43135760-A-G
• rs7119153
• ENST00000533565.1:n.130-14360T>C

Variant summary

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

The ENST00000533565.1(HNRNPKP3):​n.130-14360T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.152 in 152,220 control chromosomes in the GnomAD database, including 1,945 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 0.15 (1945 hom., cov: 32)
• Consequence: HNRNPKP3 ENST00000533565.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.602
• Publications: 1 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 = 0.184 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.130-14360T>C		intron_variant	Intron 1 of 2	4
HNRNPKP3	ENST00000770296.1	n.187-14360T>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.152 AC: 23079 AN: 152102 Hom.: 1948 Cov.: 32

Gnomad AFR AF: 0.0982

Gnomad AMI AF: 0.125

Gnomad AMR AF: 0.129

Gnomad ASJ AF: 0.154

Gnomad EAS AF: 0.00231

Gnomad SAS AF: 0.132

Gnomad FIN AF: 0.256

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.186

Gnomad OTH AF: 0.152

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

GnomAD4 genome AF: 0.152 AC: 23079 AN: 152220 Hom.: 1945 Cov.: 32 AF XY: 0.152 AC XY: 11308 AN XY: 74416

African (AFR) AF: 0.0981 AC: 4076 AN: 41550

American (AMR) AF: 0.129 AC: 1970 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.154 AC: 536 AN: 3472

East Asian (EAS) AF: 0.00231 AC: 12 AN: 5188

South Asian (SAS) AF: 0.131 AC: 633 AN: 4814

European-Finnish (FIN) AF: 0.256 AC: 2708 AN: 10592

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.186 AC: 12675 AN: 67988

Other (OTH) AF: 0.153 AC: 324 AN: 2116

Alfa AF: 0.170 Hom.: 587

Bravo AF: 0.137

Asia WGS AF: 0.0720 AC: 249 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	9.9
DANN	Benign	0.76
PhyloP100		0.60

Splicing

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

Other links and lift over

dbSNP: rs7119153; hg19: chr11-43157310;