rs10517834

Positions:

• chr4-119365628-G-C
• chr4-119365628-G-T

Variant summary

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

The ENST00000508691.1(KLHL2P1):​n.354+11397G>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.31 in 152,002 control chromosomes in the GnomAD database, including 7,468 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 0.31 (7468 hom., cov: 32)
• Consequence: KLHL2P1 ENST00000508691.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.112

Genes affected

KLHL2P1 (HGNC:44046): (kelch like family member 2 pseudogene 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.428 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
KLHL2P1	ENST00000508691.1	n.354+11397G>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.310 AC: 47103 AN: 151884 Hom.: 7465 Cov.: 32

Gnomad AFR AF: 0.277

Gnomad AMI AF: 0.282

Gnomad AMR AF: 0.293

Gnomad ASJ AF: 0.213

Gnomad EAS AF: 0.443

Gnomad SAS AF: 0.245

Gnomad FIN AF: 0.315

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.333

Gnomad OTH AF: 0.319

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

GnomAD4 genome AF: 0.310 AC: 47125 AN: 152002 Hom.: 7468 Cov.: 32 AF XY: 0.308 AC XY: 22872 AN XY: 74266

Gnomad4 AFR AF: 0.277

Gnomad4 AMR AF: 0.293

Gnomad4 ASJ AF: 0.213

Gnomad4 EAS AF: 0.443

Gnomad4 SAS AF: 0.244

Gnomad4 FIN AF: 0.315

Gnomad4 NFE AF: 0.333

Gnomad4 OTH AF: 0.317

Alfa AF: 0.301 Hom.: 897

Bravo AF: 0.314

Asia WGS AF: 0.311 AC: 1081 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	6.0
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10517834; hg19: chr4-120286783;