rs7949504

Variant names:

• chr11-43130775-G-A
• rs7949504
• ENST00000533565.1:n.130-9375C>T

Variant summary

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

The ENST00000533565.1(HNRNPKP3):​n.130-9375C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.162 in 152,142 control chromosomes in the GnomAD database, including 2,141 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 0.16 (2141 hom., cov: 32)
• Consequence: HNRNPKP3 ENST00000533565.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.110
• 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=-0.83).
• 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.130-9375C>T		intron_variant	Intron 1 of 2	4
HNRNPKP3	ENST00000770296.1	n.187-9375C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.162 AC: 24612 AN: 152024 Hom.: 2141 Cov.: 32

Gnomad AFR AF: 0.134

Gnomad AMI AF: 0.125

Gnomad AMR AF: 0.131

Gnomad ASJ AF: 0.155

Gnomad EAS AF: 0.00232

Gnomad SAS AF: 0.133

Gnomad FIN AF: 0.257

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.187

Gnomad OTH AF: 0.162

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

GnomAD4 genome AF: 0.162 AC: 24624 AN: 152142 Hom.: 2141 Cov.: 32 AF XY: 0.162 AC XY: 12054 AN XY: 74356

African (AFR) AF: 0.134 AC: 5564 AN: 41536

American (AMR) AF: 0.130 AC: 1992 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.155 AC: 536 AN: 3464

East Asian (EAS) AF: 0.00233 AC: 12 AN: 5160

South Asian (SAS) AF: 0.132 AC: 638 AN: 4820

European-Finnish (FIN) AF: 0.257 AC: 2715 AN: 10584

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

European-Non Finnish (NFE) AF: 0.186 AC: 12678 AN: 67982

Other (OTH) AF: 0.163 AC: 344 AN: 2114

Alfa AF: 0.175 Hom.: 1302

Bravo AF: 0.148

Asia WGS AF: 0.0770 AC: 266 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	3.3
DANN	Benign	0.66
PhyloP100		0.11

Splicing

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

Other links and lift over

dbSNP: rs7949504; hg19: chr11-43152325;