13-33050248-A-T

Position:

• chr13-33050248-A-T

Variant summary

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

The NM_004795.4(KL):​c.820-3519A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.665 in 152,118 control chromosomes in the GnomAD database, including 34,163 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 0.67 (34163 hom., cov: 33)
• Consequence: KL NM_004795.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.295

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=-0.8).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.752 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
KL	NM_004795.4	c.820-3519A>T		intron_variant		ENST00000380099.4
KL	XM_006719895.3	c.-102-3519A>T		intron_variant
KL	XM_047430775.1	c.820-3519A>T		intron_variant
KL	XM_047430776.1	c.820-3519A>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KL	ENST00000380099.4	c.820-3519A>T		intron_variant		1	NM_004795.4	P1
KL	ENST00000487852.1	n.828-3519A>T		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.665 AC: 101134 AN: 152002 Hom.: 34123 Cov.: 33

Gnomad AFR AF: 0.551

Gnomad AMI AF: 0.768

Gnomad AMR AF: 0.762

Gnomad ASJ AF: 0.693

Gnomad EAS AF: 0.703

Gnomad SAS AF: 0.660

Gnomad FIN AF: 0.706

Gnomad MID AF: 0.750

Gnomad NFE AF: 0.700

Gnomad OTH AF: 0.694

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

GnomAD4 genome AF: 0.665 AC: 101224 AN: 152118 Hom.: 34163 Cov.: 33 AF XY: 0.667 AC XY: 49619 AN XY: 74362

Gnomad4 AFR AF: 0.552

Gnomad4 AMR AF: 0.763

Gnomad4 ASJ AF: 0.693

Gnomad4 EAS AF: 0.704

Gnomad4 SAS AF: 0.659

Gnomad4 FIN AF: 0.706

Gnomad4 NFE AF: 0.700

Gnomad4 OTH AF: 0.695

Alfa AF: 0.575 Hom.: 1697

Bravo AF: 0.670

Asia WGS AF: 0.691 AC: 2403 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	0.77
DANN	Benign	0.87

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: rs684868; hg19: chr13-33624385;