11-43154240-G-T

Position:

• chr11-43154240-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000533565.1(HNRNPKP3):​n.130-32840C>A variant causes a intron, non coding transcript change. The variant allele was found at a frequency of 0.329 in 151,062 control chromosomes in the GnomAD database, including 8,444 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 0.33 (8444 hom., cov: 31)
• Consequence: HNRNPKP3 ENST00000533565.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: No conservation score assigned

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.412 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
HNRNPKP3	ENST00000533565.1	n.130-32840C>A		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.329 AC: 49635 AN: 150946 Hom.: 8444 Cov.: 31

Gnomad AFR AF: 0.261

Gnomad AMI AF: 0.466

Gnomad AMR AF: 0.268

Gnomad ASJ AF: 0.324

Gnomad EAS AF: 0.426

Gnomad SAS AF: 0.327

Gnomad FIN AF: 0.356

Gnomad MID AF: 0.217

Gnomad NFE AF: 0.371

Gnomad OTH AF: 0.319

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

GnomAD4 genome AF: 0.329 AC: 49643 AN: 151062 Hom.: 8444 Cov.: 31 AF XY: 0.327 AC XY: 24091 AN XY: 73716

Gnomad4 AFR AF: 0.260

Gnomad4 AMR AF: 0.268

Gnomad4 ASJ AF: 0.324

Gnomad4 EAS AF: 0.427

Gnomad4 SAS AF: 0.327

Gnomad4 FIN AF: 0.356

Gnomad4 NFE AF: 0.372

Gnomad4 OTH AF: 0.316

Alfa AF: 0.354 Hom.: 15214

Bravo AF: 0.320

Asia WGS AF: 0.347 AC: 1213 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.9
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12789205; hg19: chr11-43175790;