rs9391734

Variant names:

• chr6-32130206-G-A
• rs9391734
• NM_022110.4:c.-186C>T

Variant summary

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

The NM_022110.4(FKBPL):​c.-186C>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.106 in 204,372 control chromosomes in the GnomAD database, including 1,470 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 0.11 (1080 hom., cov: 31)
  • Exomes 𝑓: 0.088 (390 hom.)
• Consequence: FKBPL NM_022110.4 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.281
• Publications: 23 publications found

Genes affected

FKBPL (HGNC:13949): (FKBP prolyl isomerase like) The protein encoded by this gene has similarity to the immunophilin protein family, which play a role in immunoregulation and basic cellular processes involving protein folding and trafficking. The encoded protein is thought to have a potential role in the induced radioresistance. Also it appears to have some involvement in the control of the cell cycle. [provided by RefSeq, Jul 2008]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.151 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FKBPL	NM_022110.4	c.-186C>T		5_prime_UTR_variant	Exon 1 of 2	ENST00000375156.4	NP_071393.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FKBPL	ENST00000375156.4	c.-186C>T		5_prime_UTR_variant	Exon 1 of 2	1	NM_022110.4	ENSP00000364298.3

Frequencies

GnomAD3 genomes AF: 0.113 AC: 17150 AN: 151984 Hom.: 1085 Cov.: 31

Gnomad AFR AF: 0.154

Gnomad AMI AF: 0.175

Gnomad AMR AF: 0.0801

Gnomad ASJ AF: 0.126

Gnomad EAS AF: 0.0392

Gnomad SAS AF: 0.157

Gnomad FIN AF: 0.0553

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.105

Gnomad OTH AF: 0.113

GnomAD4 exome AF: 0.0883 AC: 4616 AN: 52272 Hom.: 390 Cov.: 0 AF XY: 0.0939 AC XY: 2713 AN XY: 28898

African (AFR) AF: 0.118 AC: 110 AN: 936

American (AMR) AF: 0.0793 AC: 277 AN: 3492

Ashkenazi Jewish (ASJ) AF: 0.0921 AC: 98 AN: 1064

East Asian (EAS) AF: 0.0362 AC: 94 AN: 2600

South Asian (SAS) AF: 0.140 AC: 1218 AN: 8698

European-Finnish (FIN) AF: 0.0398 AC: 58 AN: 1458

Middle Eastern (MID) AF: 0.0615 AC: 8 AN: 130

European-Non Finnish (NFE) AF: 0.0811 AC: 2541 AN: 31320

Other (OTH) AF: 0.0824 AC: 212 AN: 2574

GnomAD4 genome AF: 0.113 AC: 17148 AN: 152100 Hom.: 1080 Cov.: 31 AF XY: 0.110 AC XY: 8210 AN XY: 74336

African (AFR) AF: 0.154 AC: 6381 AN: 41470

American (AMR) AF: 0.0798 AC: 1220 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.126 AC: 438 AN: 3468

East Asian (EAS) AF: 0.0395 AC: 204 AN: 5166

South Asian (SAS) AF: 0.156 AC: 751 AN: 4814

European-Finnish (FIN) AF: 0.0553 AC: 586 AN: 10592

Middle Eastern (MID) AF: 0.0850 AC: 25 AN: 294

European-Non Finnish (NFE) AF: 0.105 AC: 7149 AN: 68002

Other (OTH) AF: 0.112 AC: 235 AN: 2102

Alfa AF: 0.100 Hom.: 1945

Bravo AF: 0.117

Asia WGS AF: 0.0720 AC: 252 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	10
DANN	Benign	0.91
PhyloP100		0.28
PromoterAI		0.059	Neutral
Mutation Taster		=300/0	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: rs9391734; hg19: chr6-32097983;