rs10213554

Variant names:

• chr4-119339630-G-A
• rs10213554

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

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 intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.681
• Publications: 6 publications found

Genes affected

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

ENSG00000294020 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000508691.1. 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
	KLHL2P1	ENST00000508691.1	TSL:6	n.126-4528G>A		intron	N/A
	ENSG00000294020	ENST00000720595.1		n.302-4528G>A		intron	N/A
	ENSG00000294020	ENST00000720596.1		n.350-4528G>A		intron	N/A

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

African (AFR) AF: 0.334 AC: 13850 AN: 41414

American (AMR) AF: 0.304 AC: 4634 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.205 AC: 712 AN: 3468

East Asian (EAS) AF: 0.389 AC: 2009 AN: 5170

South Asian (SAS) AF: 0.209 AC: 1007 AN: 4826

European-Finnish (FIN) AF: 0.298 AC: 3139 AN: 10546

Middle Eastern (MID) AF: 0.313 AC: 92 AN: 294

European-Non Finnish (NFE) AF: 0.333 AC: 22617 AN: 67934

Other (OTH) AF: 0.336 AC: 709 AN: 2110

Alfa AF: 0.315 Hom.: 1364

Bravo AF: 0.330

Asia WGS AF: 0.292 AC: 1016 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	9.0
DANN	Benign	0.37
PhyloP100		0.68

Splicing

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

Other links and lift over

dbSNP: rs10213554; hg19: chr4-120260785;