rs13096522

Variant names:

• chr3-96350694-T-A
• rs13096522
• ENST00000485383.1:n.1141T>A

Your query was ambiguous. Multiple possible variants found:

• chr3-96350694-T-A
• chr3-96350694-T-C

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000485383.1(HNRNPKP4):​n.1141T>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.196 in 1,201,736 control chromosomes in the GnomAD database, including 24,911 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 (2524 hom., cov: 32)
  • Exomes 𝑓: 0.20 (22387 hom.)
• Consequence: HNRNPKP4 ENST00000485383.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.179
• Publications: 2 publications found

Genes affected

HNRNPKP4 (HGNC:42377): (heterogeneous nuclear ribonucleoprotein K pseudogene 4)

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.44).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.24 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000485383.1. 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
	HNRNPKP4	ENST00000485383.1	TSL:6	n.1141T>A		non_coding_transcript_exon	Exon 1 of 1

Frequencies

GnomAD3 genomes AF: 0.159 AC: 24217 AN: 151996 Hom.: 2527 Cov.: 32

Gnomad AFR AF: 0.0382

Gnomad AMI AF: 0.249

Gnomad AMR AF: 0.175

Gnomad ASJ AF: 0.179

Gnomad EAS AF: 0.251

Gnomad SAS AF: 0.190

Gnomad FIN AF: 0.286

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.199

Gnomad OTH AF: 0.152

GnomAD4 exome AF: 0.202 AC: 211864 AN: 1049622 Hom.: 22387 Cov.: 15 AF XY: 0.201 AC XY: 108678 AN XY: 541552

African (AFR) AF: 0.0370 AC: 947 AN: 25620

American (AMR) AF: 0.198 AC: 8765 AN: 44186

Ashkenazi Jewish (ASJ) AF: 0.185 AC: 4362 AN: 23582

East Asian (EAS) AF: 0.252 AC: 9517 AN: 37734

South Asian (SAS) AF: 0.186 AC: 14489 AN: 77728

European-Finnish (FIN) AF: 0.273 AC: 14531 AN: 53228

Middle Eastern (MID) AF: 0.114 AC: 561 AN: 4940

European-Non Finnish (NFE) AF: 0.203 AC: 149738 AN: 736008

Other (OTH) AF: 0.192 AC: 8954 AN: 46596

GnomAD4 genome AF: 0.159 AC: 24206 AN: 152114 Hom.: 2524 Cov.: 32 AF XY: 0.162 AC XY: 12070 AN XY: 74342

African (AFR) AF: 0.0381 AC: 1584 AN: 41542

American (AMR) AF: 0.175 AC: 2667 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.179 AC: 622 AN: 3472

East Asian (EAS) AF: 0.251 AC: 1294 AN: 5150

South Asian (SAS) AF: 0.188 AC: 908 AN: 4818

European-Finnish (FIN) AF: 0.286 AC: 3023 AN: 10570

Middle Eastern (MID) AF: 0.119 AC: 35 AN: 294

European-Non Finnish (NFE) AF: 0.199 AC: 13527 AN: 67984

Other (OTH) AF: 0.151 AC: 320 AN: 2116

Alfa AF: 0.187 Hom.: 393

Bravo AF: 0.147

Asia WGS AF: 0.253 AC: 879 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.44
CADD	Benign	7.7
DANN	Benign	0.86
PhyloP100		-0.18

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs13096522;

hg19: chr3-96069538;