rs10492807

Positions:

• chr16-31768797-C-G

Variant summary

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

The ENST00000534369.1(KRBOX5):​c.4-23833C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0366 in 152,206 control chromosomes in the GnomAD database, including 278 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 0.037 (278 hom., cov: 32)
• Consequence: KRBOX5 ENST00000534369.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.14

Genes affected

KRBOX5 (HGNC:26987): (KRAB box domain containing 5) Predicted to be involved in regulation of transcription, DNA-templated. [provided by Alliance of Genome Resources, Apr 2022]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.106 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.31768797C>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
KRBOX5	ENST00000534369.1	c.4-23833C>G		intron_variant		3		ENSP00000431546.1
KRBOX5	ENST00000531864.6	n.324+14897C>G		intron_variant		2
KRBOX5	ENST00000544044.1	n.388+9331C>G		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.0366 AC: 5562 AN: 152090 Hom.: 279 Cov.: 32

Gnomad AFR AF: 0.100

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0219

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.113

Gnomad SAS AF: 0.0491

Gnomad FIN AF: 0.00367

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.00219

Gnomad OTH AF: 0.0277

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

GnomAD4 genome AF: 0.0366 AC: 5566 AN: 152206 Hom.: 278 Cov.: 32 AF XY: 0.0361 AC XY: 2684 AN XY: 74404

Gnomad4 AFR AF: 0.100

Gnomad4 AMR AF: 0.0220

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.114

Gnomad4 SAS AF: 0.0485

Gnomad4 FIN AF: 0.00367

Gnomad4 NFE AF: 0.00219

Gnomad4 OTH AF: 0.0293

Alfa AF: 0.0209 Hom.: 15

Bravo AF: 0.0406

Asia WGS AF: 0.104 AC: 360 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	2.1
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10492807; hg19: chr16-31780118;