4-119339630-G-A

Position:

• chr4-119339630-G-A

Variant summary

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

The ENST00000508691.1(KLHL2P1):​n.126-4528G>A 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 0.323 in 151,936 control chromosomes in the GnomAD database, including 8,053 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 0.32 (8053 hom., cov: 32)
• Consequence: KLHL2P1 ENST00000508691.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.681

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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.374 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KLHL2P1	ENST00000508691.1	n.126-4528G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.323 AC: 49050 AN: 151818 Hom.: 8047 Cov.: 32

Gnomad AFR AF: 0.335

Gnomad AMI AF: 0.343

Gnomad AMR AF: 0.304

Gnomad ASJ AF: 0.205

Gnomad EAS AF: 0.388

Gnomad SAS AF: 0.210

Gnomad FIN AF: 0.298

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.333

Gnomad OTH AF: 0.335

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

GnomAD4 genome AF: 0.323 AC: 49082 AN: 151936 Hom.: 8053 Cov.: 32 AF XY: 0.320 AC XY: 23777 AN XY: 74236

Gnomad4 AFR AF: 0.334

Gnomad4 AMR AF: 0.304

Gnomad4 ASJ AF: 0.205

Gnomad4 EAS AF: 0.389

Gnomad4 SAS AF: 0.209

Gnomad4 FIN AF: 0.298

Gnomad4 NFE AF: 0.333

Gnomad4 OTH AF: 0.336

Alfa AF: 0.315 Hom.: 1323

Bravo AF: 0.330

Asia WGS AF: 0.292 AC: 1016 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	9.0
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10213554; hg19: chr4-120260785;