11-43154240-G-T

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 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=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.412 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000533565.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HNRNPKP3	ENST00000533565.1	TSL:4	n.130-32840C>A		intron	N/A
	HNRNPKP3	ENST00000770296.1		n.187-32840C>A		intron	N/A
	HNRNPKP3	ENST00000770297.1		n.242-13235C>A		intron	N/A

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

African (AFR) AF: 0.260 AC: 10723 AN: 41194

American (AMR) AF: 0.268 AC: 4057 AN: 15148

Ashkenazi Jewish (ASJ) AF: 0.324 AC: 1120 AN: 3462

East Asian (EAS) AF: 0.427 AC: 2146 AN: 5030

South Asian (SAS) AF: 0.327 AC: 1566 AN: 4782

European-Finnish (FIN) AF: 0.356 AC: 3744 AN: 10506

Middle Eastern (MID) AF: 0.230 AC: 65 AN: 282

European-Non Finnish (NFE) AF: 0.372 AC: 25139 AN: 67660

Other (OTH) AF: 0.316 AC: 659 AN: 2088

Alfa AF: 0.349 Hom.: 26027

Bravo AF: 0.320

Asia WGS AF: 0.347 AC: 1213 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

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

Other links and lift over

dbSNP: rs12789205; hg19: chr11-43175790;