chr22-23931932-G-C

Variant names:

• chr22-23931932-G-C
• rs9608219

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 0.433 in 150,310 control chromosomes in the GnomAD database, including 16,736 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 0.43 (16736 hom., cov: 29)
• Consequence: KLHL5P1 intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.91
• Publications: 3 publications found

Genes affected

KLHL5P1 (HGNC:56977):

ENSG00000290199 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.64).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.568 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KLHL5P1		n.23931932G>C		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000290199	ENST00000703580.1	n.310-5412C>G		intron_variant	Intron 2 of 3
ENSG00000290199	ENST00000717616.1	n.136-5412C>G		intron_variant	Intron 1 of 2
ENSG00000290199	ENST00000717617.1	n.136-5412C>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.433 AC: 65015 AN: 150200 Hom.: 16725 Cov.: 29

Gnomad AFR AF: 0.155

Gnomad AMI AF: 0.605

Gnomad AMR AF: 0.500

Gnomad ASJ AF: 0.463

Gnomad EAS AF: 0.448

Gnomad SAS AF: 0.585

Gnomad FIN AF: 0.605

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.546

Gnomad OTH AF: 0.438

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

GnomAD4 genome AF: 0.433 AC: 65024 AN: 150310 Hom.: 16736 Cov.: 29 AF XY: 0.441 AC XY: 32358 AN XY: 73320

African (AFR) AF: 0.154 AC: 6367 AN: 41278

American (AMR) AF: 0.500 AC: 7541 AN: 15074

Ashkenazi Jewish (ASJ) AF: 0.463 AC: 1593 AN: 3442

East Asian (EAS) AF: 0.448 AC: 2236 AN: 4994

South Asian (SAS) AF: 0.586 AC: 2770 AN: 4724

European-Finnish (FIN) AF: 0.605 AC: 6244 AN: 10320

Middle Eastern (MID) AF: 0.466 AC: 135 AN: 290

European-Non Finnish (NFE) AF: 0.546 AC: 36675 AN: 67194

Other (OTH) AF: 0.438 AC: 917 AN: 2092

Alfa AF: 0.478 Hom.: 2334

Bravo AF: 0.415

Asia WGS AF: 0.520 AC: 1807 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.64
CADD	Benign	12
DANN	Benign	0.85
PhyloP100		1.9

Splicing

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

Other links and lift over

dbSNP: rs9608219; hg19: chr22-24274119; COSMIC: COSV71571554;