chr4-39410641-C-T

Variant names:

• chr4-39410641-C-T
• rs1982738
• NM_175737.4:c.825+2867C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_175737.4(KLB):​c.825+2867C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.236 in 152,044 control chromosomes in the GnomAD database, including 4,509 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 0.24 (4509 hom., cov: 31)
• Consequence: KLB NM_175737.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.22
• Publications: 4 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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.54).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.351 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KLB	NM_175737.4	MANE Select	c.825+2867C>T		intron	N/A	NP_783864.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KLB	ENST00000257408.5	TSL:1 MANE Select	c.825+2867C>T		intron	N/A	ENSP00000257408.4

Frequencies

GnomAD3 genomes AF: 0.236 AC: 35825 AN: 151926 Hom.: 4489 Cov.: 31

Gnomad AFR AF: 0.311

Gnomad AMI AF: 0.187

Gnomad AMR AF: 0.186

Gnomad ASJ AF: 0.173

Gnomad EAS AF: 0.365

Gnomad SAS AF: 0.203

Gnomad FIN AF: 0.240

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.198

Gnomad OTH AF: 0.218

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

GnomAD4 genome AF: 0.236 AC: 35881 AN: 152044 Hom.: 4509 Cov.: 31 AF XY: 0.236 AC XY: 17520 AN XY: 74308

African (AFR) AF: 0.312 AC: 12913 AN: 41442

American (AMR) AF: 0.186 AC: 2837 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.173 AC: 602 AN: 3472

East Asian (EAS) AF: 0.365 AC: 1891 AN: 5180

South Asian (SAS) AF: 0.202 AC: 974 AN: 4824

European-Finnish (FIN) AF: 0.240 AC: 2539 AN: 10562

Middle Eastern (MID) AF: 0.205 AC: 60 AN: 292

European-Non Finnish (NFE) AF: 0.198 AC: 13426 AN: 67970

Other (OTH) AF: 0.222 AC: 469 AN: 2112

Alfa AF: 0.224 Hom.: 498

Bravo AF: 0.235

Asia WGS AF: 0.340 AC: 1180 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.54
CADD	Benign	14
DANN	Benign	0.82
PhyloP100		1.2
Mutation Taster		=100/0	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: rs1982738; hg19: chr4-39412261;