11-43154240-G-T

Variant names:

• chr11-43154240-G-T
• rs12789205
• ENST00000533565.1:n.130-32840C>A

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 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
• Clinical Significance: Not reported in ClinVar
• Conservation: No conservation score assigned

Genes affected

HNRNPKP3 (HGNC:):

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HNRNPKP3	ENST00000533565.1	n.130-32840C>A		intron_variant	Intron 1 of 2	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;