chr4-39446909-G-A

Variant names:

• chr4-39446909-G-A
• rs17618244
• NM_175737.4:c.2183G>A

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NM_175737.4(KLB):​c.2183G>A​(p.Arg728Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.183 in 1,605,394 control chromosomes in the GnomAD database, including 27,915 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.16 (2245 hom., cov: 33)
  • Exomes 𝑓: 0.19 (25670 hom.)
• Consequence: KLB NM_175737.4 missense
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: 0.426
• Publications: 48 publications found

Genes affected

KLB (HGNC:15527): (klotho beta) Enables fibroblast growth factor binding activity and fibroblast growth factor receptor binding activity. Predicted to be involved in fibroblast growth factor receptor signaling pathway. Predicted to act upstream of or within positive regulation of MAPKKK cascade by fibroblast growth factor receptor signaling pathway and positive regulation of cell population proliferation. Predicted to be located in plasma membrane. Predicted to be active in endoplasmic reticulum. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -20 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=0.0029337704).
• BP6: Variant 4-39446909-G-A is Benign according to our data. Variant chr4-39446909-G-A is described in ClinVar as Benign. ClinVar VariationId is 1601724.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.21 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_175737.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KLB	NM_175737.4	MANE Select	c.2183G>A	p.Arg728Gln	missense	Exon 4 of 5	NP_783864.1	Q86Z14

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KLB	ENST00000257408.5	TSL:1 MANE Select	c.2183G>A	p.Arg728Gln	missense	Exon 4 of 5	ENSP00000257408.4	Q86Z14
	KLB	ENST00000859482.1		c.2156G>A	p.Arg719Gln	missense	Exon 4 of 5	ENSP00000529541.1

Frequencies

GnomAD3 genomes AF: 0.159 AC: 24135 AN: 152168 Hom.: 2243 Cov.: 33

Gnomad AFR AF: 0.0719

Gnomad AMI AF: 0.159

Gnomad AMR AF: 0.216

Gnomad ASJ AF: 0.254

Gnomad EAS AF: 0.178

Gnomad SAS AF: 0.173

Gnomad FIN AF: 0.156

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.190

Gnomad OTH AF: 0.203

GnomAD2 exomes AF: 0.183 AC: 43531 AN: 237952 AF XY: 0.184

Gnomad AFR exome AF: 0.0707

Gnomad AMR exome AF: 0.198

Gnomad ASJ exome AF: 0.255

Gnomad EAS exome AF: 0.185

Gnomad FIN exome AF: 0.165

Gnomad NFE exome AF: 0.191

Gnomad OTH exome AF: 0.196

GnomAD4 exome AF: 0.186 AC: 269987 AN: 1453108 Hom.: 25670 Cov.: 34 AF XY: 0.186 AC XY: 134194 AN XY: 723124

African (AFR) AF: 0.0725 AC: 2424 AN: 33454

American (AMR) AF: 0.202 AC: 9013 AN: 44518

Ashkenazi Jewish (ASJ) AF: 0.249 AC: 6463 AN: 25940

East Asian (EAS) AF: 0.182 AC: 7230 AN: 39682

South Asian (SAS) AF: 0.171 AC: 14685 AN: 85974

European-Finnish (FIN) AF: 0.162 AC: 7525 AN: 46512

Middle Eastern (MID) AF: 0.210 AC: 1210 AN: 5758

European-Non Finnish (NFE) AF: 0.189 AC: 210032 AN: 1111018

Other (OTH) AF: 0.189 AC: 11405 AN: 60252

GnomAD4 genome AF: 0.158 AC: 24132 AN: 152286 Hom.: 2245 Cov.: 33 AF XY: 0.157 AC XY: 11687 AN XY: 74472

African (AFR) AF: 0.0717 AC: 2980 AN: 41568

American (AMR) AF: 0.216 AC: 3301 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.254 AC: 880 AN: 3470

East Asian (EAS) AF: 0.178 AC: 920 AN: 5174

South Asian (SAS) AF: 0.172 AC: 830 AN: 4832

European-Finnish (FIN) AF: 0.156 AC: 1654 AN: 10614

Middle Eastern (MID) AF: 0.245 AC: 72 AN: 294

European-Non Finnish (NFE) AF: 0.190 AC: 12922 AN: 68006

Other (OTH) AF: 0.202 AC: 428 AN: 2114

Alfa AF: 0.180 Hom.: 1761

Bravo AF: 0.160

TwinsUK AF: 0.184 AC: 682

ALSPAC AF: 0.184 AC: 710

ESP6500AA AF: 0.0682 AC: 300

ESP6500EA AF: 0.191 AC: 1645

ExAC AF: 0.176 AC: 21236

Asia WGS AF: 0.175 AC: 610 AN: 3478

EpiCase AF: 0.198

EpiControl AF: 0.204

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, multiple submitters, no conflicts

Pathogenic	VUS	Benign	Condition
-	-	2	not provided (2)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.073
BayesDel_addAF	Benign	-0.75	T
BayesDel_noAF	Benign	-0.71
CADD	Benign	7.6
DANN	Uncertain	0.98
DEOGEN2	Benign	0.019	T
Eigen	Benign	-0.73
Eigen_PC	Benign	-0.78
FATHMM_MKL	Benign	0.036	N
LIST_S2	Benign	0.61	T
MetaRNN	Benign	0.0029	T
MetaSVM	Benign	-0.96	T
MutationAssessor	Benign	1.4	L
PhyloP100		0.43
PrimateAI	Benign	0.24	T
PROVEAN	Benign	-0.18	N
REVEL	Benign	0.047
Sift	Benign	0.32	T
Sift4G	Benign	0.26	T
Polyphen		0.66	P
Vest4		0.075
MPC		0.68
ClinPred		0.0093	T
GERP RS		0.47
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
Varity_R		0.21
gMVP		0.56
Mutation Taster		=94/6	polymorphism (auto)

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

Other links and lift over

dbSNP: rs17618244; hg19: chr4-39448529; COSMIC: COSV57300791;