rs2141349

chr16-31718231-A-Cchr16-31718231-A-T

Variant summary

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

The NM_001130913.2(KRBOX5):c.4-4395A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.608 in 151,862 control chromosomes in the GnomAD database, including 29,051 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 0.61 (29051 hom., cov: 31)
• Consequence: KRBOX5 NM_001130913.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.491

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.697 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
KRBOX5	NM_001130913.2	c.4-4395A>C		intron_variant		ENST00000316491.14

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KRBOX5	ENST00000316491.14	c.4-4395A>C		intron_variant		1	NM_001130913.2

Frequencies

GnomAD3 genomes AF: 0.608 AC: 92208 AN: 151744 Hom.: 29036 Cov.: 31

Gnomad AFR AF: 0.513

Gnomad AMI AF: 0.909

Gnomad AMR AF: 0.530

Gnomad ASJ AF: 0.770

Gnomad EAS AF: 0.320

Gnomad SAS AF: 0.456

Gnomad FIN AF: 0.606

Gnomad MID AF: 0.709

Gnomad NFE AF: 0.702

Gnomad OTH AF: 0.599

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

GnomAD4 genome AF: 0.608 AC: 92259 AN: 151862 Hom.: 29051 Cov.: 31 AF XY: 0.602 AC XY: 44688 AN XY: 74216

Gnomad4 AFR AF: 0.513

Gnomad4 AMR AF: 0.530

Gnomad4 ASJ AF: 0.770

Gnomad4 EAS AF: 0.319

Gnomad4 SAS AF: 0.456

Gnomad4 FIN AF: 0.606

Gnomad4 NFE AF: 0.702

Gnomad4 OTH AF: 0.594

Alfa AF: 0.546 Hom.: 1644

Bravo AF: 0.596

Asia WGS AF: 0.394 AC: 1377 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	2.6
Dann	Benign	0.81
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs2141349; hg19: chr16-31729552;