rs516306

chr13-33026139-T-C

Variant summary

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

The NM_004795.4(KL):c.819+8880T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.316 in 152,012 control chromosomes in the GnomAD database, including 8,799 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 (8799 hom., cov: 32)
• Consequence: KL NM_004795.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.39

Genes affected

KL (HGNC:6344): (klotho) This gene encodes a type-I membrane protein that is related to beta-glucosidases. Reduced production of this protein has been observed in patients with chronic renal failure (CRF), and this may be one of the factors underlying the degenerative processes (e.g., arteriosclerosis, osteoporosis, and skin atrophy) seen in CRF. Also, mutations within this protein have been associated with ageing and bone loss. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.429 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
KL	NM_004795.4	c.819+8880T>C		intron_variant		ENST00000380099.4
KL	XM_006719895.3	c.-103+9826T>C		intron_variant
KL	XM_047430775.1	c.819+8880T>C		intron_variant
KL	XM_047430776.1	c.819+8880T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KL	ENST00000380099.4	c.819+8880T>C		intron_variant		1	NM_004795.4	P1
KL	ENST00000487852.1	n.827+8880T>C		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.316 AC: 47960 AN: 151894 Hom.: 8789 Cov.: 32

Gnomad AFR AF: 0.145

Gnomad AMI AF: 0.379

Gnomad AMR AF: 0.437

Gnomad ASJ AF: 0.372

Gnomad EAS AF: 0.175

Gnomad SAS AF: 0.243

Gnomad FIN AF: 0.380

Gnomad MID AF: 0.429

Gnomad NFE AF: 0.393

Gnomad OTH AF: 0.338

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

GnomAD4 genome AF: 0.316 AC: 47987 AN: 152012 Hom.: 8799 Cov.: 32 AF XY: 0.315 AC XY: 23388 AN XY: 74318

Gnomad4 AFR AF: 0.145

Gnomad4 AMR AF: 0.437

Gnomad4 ASJ AF: 0.372

Gnomad4 EAS AF: 0.175

Gnomad4 SAS AF: 0.241

Gnomad4 FIN AF: 0.380

Gnomad4 NFE AF: 0.393

Gnomad4 OTH AF: 0.342

Alfa AF: 0.334 Hom.: 1740

Bravo AF: 0.316

Asia WGS AF: 0.260 AC: 905 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	0.55
Dann	Benign	0.45

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: rs516306; hg19: chr13-33600277;